Andrej Sali, PhD
Professor
Bioengineering
School of Pharmacy

This research contributes to structure-based functional annotation of proteins and thus enhances the impact of genome sequencing, structural genomics, and functional genomics on biology and medicine.

• Structural basis of prostaglandin efflux by MRP4.
  Nature structural & molecular biology 2024 Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM
• Integrative spatiotemporal map of nucleocytoplasmic transport.
  bioRxiv : the preprint server for biology 2024 Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A
• Structures, functions and adaptations of the human LINE-1 ORF2 protein.
  Nature 2023 Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, …
• Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
  bioRxiv : the preprint server for biology 2023 Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA
• Implications of a multiscale structure of the yeast nuclear pore complex.
  Molecular cell 2023 Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP
• Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
  Research square 2023 Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, …
• Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
  bioRxiv : the preprint server for biology 2023 Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, …
• Soft X-ray Tomography for Mapping and Quantifying Intracellular Organelle Interactions.
  Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada 2023 Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Gros ML, White KL, Larabell CA
• Conformational Dynamics of the Activated GLP-1 Receptor-Gs Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling.
  ACS central science 2023 Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W
• Dynamic molecular mechanism of the nuclear pore complex permeability barrier.
  bioRxiv : the preprint server for biology 2023 Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH
• In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography.
  Research square 2023 Li W, Li A, Yu B, Zhang X, Liu X, White K, Stevens R, Baumeister W, Sali A, Jasnin M, Sun L
• ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
  Journal of molecular biology 2023 Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, …
• Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
  Nature structural & molecular biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM
• Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
  bioRxiv : the preprint server for biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM
• RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
  Nucleic acids research 2023 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, …
• A quantitative map of nuclear pore assembly reveals two distinct mechanisms.
  Nature 2023 Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J
• Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.
  Biophysical reviews 2022 Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C
• RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
  Protein science : a publication of the Protein Society 2022 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, …
• Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.
  Biomolecules 2022 Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C
• An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms.
  PloS one 2022 Li A, Zhang S, Loconte V, Liu Y, Ekman A, Thompson GJ, Sali A, Stevens RC, White K, Singla J, Sun L
• Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic beta cells.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Guo A, Zhang J, He B, Li A, Sun T, Li W, Wang J, Tai R, Liu Y, Qian Z, Fan J, Sali A, Stevens RC, Jiang H
• Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain.
  eLife 2022 Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC
• Integrative structure determination of histones H3 and H4 using genetic interactions.
  The FEBS journal 2022 Echeverria I, Braberg H, Krogan NJ, Sali A
• The YΦ motif defines the structure-activity relationships of human 20S proteasome activators.
  Nature communications 2022 Opoku-Nsiah KA, de la Pena AH, Williams SK, Chopra N, Sali A, Lander GC, Gestwicki JE
• Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.
  Structure (London, England : 1993) 2022 Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA
• Integration of software tools for integrative modeling of biomolecular systems.
  Journal of structural biology 2022 Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A
• Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF
• From systems to structure - using genetic data to model protein structures.
  Nature reviews. Genetics 2022 Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ
• Comprehensive structure and functional adaptations of the yeast nuclear pore complex.
  Cell 2022 Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez…
• Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape.
  eLife 2021 Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein …
• New system for archiving integrative structures.
  Acta crystallographica. Section D, Structural biology 2021 Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM
• Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb.
  eLife 2021 Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K
• RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.
  Protein science : a publication of the Protein Society 2021 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Kramer Green R, Guranovic V, Henry J, Hudson BP, Lawson…
• Bayesian metamodeling of complex biological systems across varying representations.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A
• IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics.
  Molecular & cellular proteomics : MCP 2021 Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC
• Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.
  Molecular & cellular proteomics : MCP 2021 Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ
• The EBF1-PDGFRB T681I mutation is highly resistant to imatinib and dasatinib in vitro and detectable in clinical samples prior to treatment.
  Haematologica 2021 Tran TH, Nguyen JV, Stecula A, Akutagawa J, Moorman AV, Braun BS, Sali A, Mullighan CG, Shah NP, Dai Y, Devidas M, Roberts KG, Smith CC, Loh ML
• Integrative analysis reveals unique structural and functional features of the Smc5/6 complex.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Yu Y, Li S, Ser Z, Sanyal T, Choi K, Wan B, Kuang H, Sali A, Kentsis A, Patel DJ, Zhao X
• CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.
  eLife 2021 Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA
• From integrative structural biology to cell biology.
  The Journal of biological chemistry 2021 Sali A
• Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.
  bioRxiv : the preprint server for biology 2021 Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein …
• Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer.
  ACS chemical biology 2021 Salcedo EC, Winter MB, Khuri N, Knudsen GM, Sali A, Craik CS
• RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.
  Nucleic acids research 2021 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Christie CH, Dalenberg K, Di Costanzo L, Duarte JM, Dutta S, Feng Z, Ganesan S, Goodsell DS, Ghosh S, Green RK, Guranovic V, Guzenko D, …
• The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex.
  Structure (London, England : 1993) 2021 Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC
• Protein Structure Modeling with MODELLER.
  Methods in molecular biology (Clifton, N.J.) 2021 Webb B, Sali A
• Genetic interaction mapping informs integrative structure determination of protein complexes.
  Science (New York, N.Y.) 2020 Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D…
• Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography.
  Science advances 2020 White KL, Singla J, Loconte V, Chen JH, Ekman A, Sun L, Zhang X, Francis JP, Li A, Lin W, Tseng K, McDermott G, Alber F, Sali A, Larabell C, Stevens RC
• Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.
  Protein science : a publication of the Protein Society 2020 Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor…
• Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.
  Structure (London, England : 1993) 2020 Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O…
• Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality.
  The Journal of cell biology 2020 Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD
• Structural basis of CD4 downregulation by HIV-1 Nef.
  Nature structural & molecular biology 2020 Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X
• Integrative structure and function of the yeast exocyst complex.
  Protein science : a publication of the Protein Society 2020 Ganesan SJ, Feyder MJ, Chemmama IE, Fang F, Rout MP, Chait BT, Shi Y, Munson M, Sali A
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, …
• Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L
• Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
  Structure (London, England : 1993) 2019 Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL…
• SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange.
  Progress in biophysics and molecular biology 2019 Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A
• Archiving and disseminating integrative structure models.
  Journal of biomolecular NMR 2019 Vallat B, Webb B, Westbrook J, Sali A, Berman HM
• Principles for Integrative Structural Biology Studies.
  Cell 2019 Rout MP, Sali A
• Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly.
  Journal of the American Chemical Society 2019 Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF
• Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone.
  eLife 2019 Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM
• Modeling Biological Complexes Using Integrative Modeling Platform.
  Methods in molecular biology (Clifton, N.J.) 2019 Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A
• Optimizing model representation for integrative structure determination of macromolecular assemblies.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Viswanath S, Sali A
• Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.
  PloS one 2018 Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A
• Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.
  Structure (London, England : 1993) 2018 Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R
• Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.
  Nature structural & molecular biology 2018 Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, Chait BT, Asturias FJ, Roeder RG
• Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.
  Methods in enzymology 2018 Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC
• Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.
  Cell 2018 Yoshizawa T, Ali R, Jiou J, Fung HYJ, Burke KA, Kim SJ, Lin Y, Peeples WB, Saltzberg D, Soniat M, Baumhardt JM, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, Chook YM
• Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.
  Structure (London, England : 1993) 2018 Vallat B, Webb B, Westbrook JD, Sali A, Berman HM
• Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.
  Cell 2018 Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC
• Integrative structure and functional anatomy of a nuclear pore complex.
  Nature 2018 Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, …
• Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures.
  Scientific reports 2018 Guy AJ, Irani V, Beeson JG, Webb B, Sali A, Richards JS, Ramsland PA
• Prediction of enzymatic pathways by integrative pathway mapping.
  eLife 2018 Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, …
• Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.
  Biophysical journal 2017 Viswanath S, Chemmama IE, Cimermancic P, Sali A
• Immunoproteasome functions explained by divergence in cleavage specificity and regulation.
  eLife 2017 Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS
• Integrative structure modeling with the Integrative Modeling Platform.
  Protein science : a publication of the Protein Society 2017 Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A
• Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Jahangiri A, Nguyen A, Chandra A, Sidorov MK, Yagnik G, Rick J, Han SW, Chen W, Flanigan PM, Schneidman-Duhovny D, Mascharak S, De Lay M, Imber B, Park CC, Matsumoto K, Lu K, Bergers G, Sali A, Weiss …
• PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
  Structure (London, England : 1993) 2017 Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J
• 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.
  Acta crystallographica. Section D, Structural biology 2017 Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, …
• The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.
  Molecular biology of the cell 2017 Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG
• The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress.
  The Journal of biological chemistry 2017 Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky SD, Ye Y, Sali A, Huang L
• Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer.
  Biochemistry 2017 Stecula A, Schlessinger A, Giacomini KM, Sali A
• Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1.
  Journal of chemical information and modeling 2017 Khuri N, Zur AA, Wittwer MB, Lin L, Yee SW, Sali A, Giacomini KM
• Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.
  Cell reports 2017 Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ
• Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages.
  PloS one 2017 Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L
• Discovery of Competitive and Noncompetitive Ligands of the Organic Cation Transporter 1 (OCT1; SLC22A1).
  Journal of medicinal chemistry 2017 Chen EC, Khuri N, Liang X, Stecula A, Chien HC, Yee SW, Huang Y, Sali A, Giacomini KM
• Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.
  Molecular & cellular proteomics : MCP 2017 Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold…
• Lineage-specific proteins essential for endocytosis in trypanosomes.
  Journal of cell science 2017 Manna PT, Obado SO, Boehm C, Gadelha C, Sali A, Chait BT, Rout MP, Field MC
• Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.
  Structure (London, England : 1993) 2017 Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J
• Protein Structure Modeling with MODELLER.
  Methods in molecular biology (Clifton, N.J.) 2017 Webb B, Sali A
• A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions.
  The journal of physical chemistry. B 2016 Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A
• Editorial overview: Biophysical and molecular biological methods.
  Current opinion in structural biology 2016 Fromme P, Sali A
• Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23.
  BMC bioinformatics 2016 Barkan DT, Cheng XL, Celino H, Tran TT, Bhandari A, Craik CS, Sali A, Smythe ML
• Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.
  Cell 2016 Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP
• Comparative Protein Structure Modeling Using MODELLER.
  Current protocols in protein science 2016 Webb B, Sali A
• Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions.
  Journal of virology 2016 Watts JC, Giles K, Saltzberg DJ, Dugger BN, Patel S, Oehler A, Bhardwaj S, Sali A, Prusiner SB
• Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
  eLife 2016 Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH
• Simple rules for passive diffusion through the nuclear pore complex.
  The Journal of cell biology 2016 Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP
• Comparative Protein Structure Modeling Using MODELLER.
  Current protocols in bioinformatics 2016 Webb B, Sali A
• Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
  Proteins 2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie …
• Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling.
  Molecular & cellular proteomics : MCP 2016 Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J
• FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.
  Nucleic acids research 2016 Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A
• Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D
• A phosphotyrosine switch regulates organic cation transporters.
  Nature communications 2016 Sprowl JA, Ong SS, Gibson AA, Hu S, Du G, Lin W, Li L, Bharill S, Ness RA, Stecula A, Offer SM, Diasio RB, Nies AT, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens JHM, Isacoff EY, Sali A,…
• Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure.
  Journal of structural biology 2016 Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A
• CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.
  Journal of molecular biology 2016 Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A
• Novel TKI-resistant BCR-ABL1 gatekeeper residue mutations retain in vitro sensitivity to axitinib.
  Leukemia 2015 Lasater EA, Massi ES, Stecula A, Politi J, Tan SK, Smith CC, Gunthorpe M, Holmes JP, Chehab F, Sali A, Shah NP
• Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer.
  The Journal of biological chemistry 2015 LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM
• Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.
  Journal of medicinal chemistry 2015 Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA
• A strategy for dissecting the architectures of native macromolecular assemblies.
  Nature methods 2015 Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT
• Molecular architecture of the yeast Mediator complex.
  eLife 2015 Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD
• Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.
  Molecular cell 2015 Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J
• Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
  PLoS computational biology 2015 Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P
• Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data.
  PloS one 2015 Roy Choudhury A, Sikorska E, van den Boom J, Bayer P, Popenda L, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novic M
• Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.
  Biophysical journal 2015 Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A
• FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors.
  Leukemia 2015 Smith CC, Lin K, Stecula A, Sali A, Shah NP
• Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
  Structure (London, England : 1993) 2015 Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, …
• Growing an editorial board for an ever expanding field.
  Structure (London, England : 1993) 2015 Lima CD, Sali A, Kostic M
• Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.
  Current protocols in bioinformatics 2015 Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ
• Ring closure activates yeast γTuRC for species-specific microtubule nucleation.
  Nature structural & molecular biology 2015 Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA
• Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex.
  Chemistry & biology 2014 Politis A, Schmidt C, Tjioe E, Sandercock AM, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson CV
• A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.
  PLoS computational biology 2014 Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA
• Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex.
  Cell 2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N
• Comparative Protein Structure Modeling Using MODELLER.
  Current protocols in bioinformatics 2014 Webb B, Sali A
• Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex.
  Cell 2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N
• Uncertainty in integrative structural modeling.
  Current opinion in structural biology 2014 Schneidman-Duhovny D, Pellarin R, Sali A
• Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.
  Molecular & cellular proteomics : MCP 2014 Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT
• Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data.
  Molecular & cellular proteomics : MCP 2014 Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A
• Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.
  Molecular & cellular proteomics : MCP 2014 Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A
• Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.
  Journal of molecular biology 2014 Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F
• Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.
  Structure (London, England : 1993) 2014 Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF
• Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.
  Molecular & cellular proteomics : MCP 2014 Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S
• Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.
  Cell 2014 Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA
• Prediction of substrates for glutathione transferases by covalent docking.
  Journal of chemical information and modeling 2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A
• Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone.
  Journal of molecular biology 2014 Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA
• Modeling of proteins and their assemblies with the Integrative Modeling Platform.
  Methods in molecular biology (Clifton, N.J.) 2014 Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A
• Protein structure modeling with MODELLER.
  Methods in molecular biology (Clifton, N.J.) 2014 Webb B, Sali A
• SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes.
  Journal of synchrotron radiation 2013 Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M
• ModBase, a database of annotated comparative protein structure models and associated resources.
  Nucleic acids research 2013 Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A
• High-resolution network biology: connecting sequence with function.
  Nature reviews. Genetics 2013 Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ
• Recovering a representative conformational ensemble from underdetermined macromolecular structural data.
  Journal of the American Chemical Society 2013 Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D
• Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
  PLoS computational biology 2013 Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA
• Optimized atomic statistical potentials: assessment of protein interfaces and loops.
  Bioinformatics (Oxford, England) 2013 Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A
• Mapping polymerization and allostery of hemoglobin S using point mutations.
  The journal of physical chemistry. B 2013 Weinkam P, Sali A
• Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.
  Biochemistry 2013 Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM
• Structure-guided discovery of new deaminase enzymes.
  Journal of the American Chemical Society 2013 Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM
• Celebrating 20 years of Structure.
  Structure (London, England : 1993) 2013 Lima CD, Sali A, Kostic M
• Accurate SAXS profile computation and its assessment by contrast variation experiments.
  Biophysical journal 2013 Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A
• Consequences of domain insertion on sequence-structure divergence in a superfold.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN
• Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.
  Structure (London, England : 1993) 2013 Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM
• Structural basis for alternating access of a eukaryotic calcium/proton exchanger.
  Nature 2013 Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM
• Evolution of modular intraflagellar transport from a coatomer-like progenitor.
  Proceedings of the National Academy of Sciences of the United States of America 2013 van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA
• Crystal structure of a eukaryotic phosphate transporter.
  Nature 2013 Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM
• Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM
• Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.
  Structure (London, England : 1993) 2013 Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout…
• All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins.
  Structure (London, England : 1993) 2013 Guttman M, Weinkam P, Sali A, Lee KK
• Biochemistry. Integrative structural biology.
  Science (New York, N.Y.) 2013 Ward AB, Sali A, Wilson IA
• Coordinating the impact of structural genomics on the human α-helical transmembrane proteome.
  Nature structural & molecular biology 2013 Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A
• Discovery of potent, selective multidrug and toxin extrusion transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling.
  Journal of medicinal chemistry 2013 Wittwer MB, Zur AA, Khuri N, Kido Y, Kosaka A, Zhang X, Morrissey KM, Sali A, Huang Y, Giacomini KM
• Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.
  Journal of the American Chemical Society 2013 Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM
• Molecular modeling and ligand docking for solute carrier (SLC) transporters.
  Current topics in medicinal chemistry 2013 Schlessinger A, Khuri N, Giacomini KM, Sali A
• Impact of mutations on the allosteric conformational equilibrium.
  Journal of molecular biology 2012 Weinkam P, Chen YC, Pons J, Sali A
• Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists.
  PloS one 2012 Kolb P, Phan K, Gao ZG, Marko AC, Sali A, Jacobson KA
• Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A
• A method for integrative structure determination of protein-protein complexes.
  Bioinformatics (Oxford, England) 2012 Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A
• Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.
  Biomacromolecules 2012 Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S
• In support of the BMRB.
  Nature structural & molecular biology 2012 Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, …
• Strategic protein target analysis for developing drugs to stop dental caries.
  Advances in dental research 2012 Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD
• High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach.
  The Journal of biological chemistry 2012 Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A
• Integrative structural modeling with small angle X-ray scattering profiles.
  BMC structural biology 2012 Schneidman-Duhovny D, Kim SJ, Sali A
• Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.
  Proteins 2012 Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, …
• Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.
  Molecular & cellular proteomics : MCP 2012 Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL
• SALIGN: a web server for alignment of multiple protein sequences and structures.
  Bioinformatics (Oxford, England) 2012 Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS
• Facile backbone structure determination of human membrane proteins by NMR spectroscopy.
  Nature methods 2012 Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu EJ, Blain KY, Esquivies L, Kwon JH, Balana B, Pieper U, Sali A, Slesinger PA, Kwiatkowski W, Riek R, Choe S
• Structure-based model of allostery predicts coupling between distant sites.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Weinkam P, Pons J, Sali A
• Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein.
  Biological chemistry 2012 Puizdar V, Zajc T, Zerovnik E, Renko M, Pieper U, Eswar N, Sali A, Dolenc I, Turk V
• Structure-function mapping of a heptameric module in the nuclear pore complex.
  The Journal of cell biology 2012 Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP
• Outcome of the first electron microscopy validation task force meeting.
  Structure (London, England : 1993) 2012 Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder …
• Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W
• Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.
  PLoS biology 2012 Russel D, Lasker K, Webb B, Velázquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A
• Macromolecular assembly structures by comparative modeling and electron microscopy.
  Methods in molecular biology (Clifton, N.J.) 2012 Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A
• Virtual ligand screening against comparative protein structure models.
  Methods in molecular biology (Clifton, N.J.) 2012 Fan H, Irwin JJ, Sali A
• Global landscape of HIV-human protein complexes.
  Nature 2011 Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey…
• Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.
  Nature 2011 Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, …
• The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Pathare GR, Nagy I, Bohn S, Unverdorben P, Hubert A, Körner R, Nickell S, Lasker K, Sali A, Tamura T, Nishioka T, Förster F, Baumeister W, Bracher A
• Statistical potential for modeling and ranking of protein-ligand interactions.
  Journal of chemical information and modeling 2011 Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A
• The Enzyme Function Initiative.
  Biochemistry 2011 Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV
• Structure meets the membrane.
  Structure (London, England : 1993) 2011 Lima C, Sali A, Kostic M
• UCSF Chimera, MODELLER, and IMP: an integrated modeling system.
  Journal of structural biology 2011 Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE
• Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
  Nature chemical biology 2011 Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK
• Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A
• Discovery of a cytokinin deaminase.
  ACS chemical biology 2011 Goble AM, Fan H, Sali A, Raushel FM
• MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.
  Nucleic acids research 2011 Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A
• Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat.
  The Journal of cell biology 2011 Field MC, Sali A, Rout MP
• A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.
  Molecular & cellular proteomics : MCP 2011 Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C
• Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.
  Proteins 2011 Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, …
• Catalytic mechanism and three-dimensional structure of adenine deaminase.
  Biochemistry 2011 Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM
• Enzymatic deamination of the epigenetic base N-6-methyladenine.
  Journal of the American Chemical Society 2011 Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM
• Modeling of proteins and their assemblies with the integrative modeling platform.
  Methods in molecular biology (Clifton, N.J.) 2011 Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A
• ModBase, a database of annotated comparative protein structure models, and associated resources.
  Nucleic acids research 2010 Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, …
• Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.
  Proteins 2010 Lasker K, Sali A, Wolfson HJ
• Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
  Protein science : a publication of the Protein Society 2010 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A
• Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin.
  Pharmacogenetics and genomics 2010 Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM
• Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
  Proteins 2010 Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, …
• Macromolecular docking restrained by a small angle X-ray scattering profile.
  Journal of structural biology 2010 Schneidman-Duhovny D, Hammel M, Sali A
• Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.
  Proteins 2010 Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, …
• FoXS: a web server for rapid computation and fitting of SAXS profiles.
  Nucleic acids research 2010 Schneidman-Duhovny D, Hammel M, Sali A
• Integrative structure modeling of macromolecular assemblies from proteomics data.
  Molecular & cellular proteomics : MCP 2010 Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A
• Prediction of protease substrates using sequence and structure features.
  Bioinformatics (Oxford, England) 2010 Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A
• Toward an integrated structural model of the 26S proteasome.
  Molecular & cellular proteomics : MCP 2010 Förster F, Lasker K, Nickell S, Sali A, Baumeister W
• Function of human Rh based on structure of RhCG at 2.1 A.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM
• Comparison of human solute carriers.
  Protein science : a publication of the Protein Society 2010 Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A
• The overlap of small molecule and protein binding sites within families of protein structures.
  PLoS computational biology 2010 Davis FP, Sali A
• Comprehensive molecular structure of the eukaryotic ribosome.
  Structure (London, England : 1993) 2009 Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J
• Molecular docking screens using comparative models of proteins.
  Journal of chemical information and modeling 2009 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A
• Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.
  Pharmacogenomics 2009 Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM
• A survey of integral alpha-helical membrane proteins.
  Journal of structural and functional genomics 2009 Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A
• Global motions of the nuclear pore complex: insights from elastic network models.
  PLoS computational biology 2009 Lezon TR, Sali A, Bahar I
• An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
  Biochemical and biophysical research communications 2009 Förster F, Lasker K, Beck F, Nickell S, Sali A, Baumeister W
• Alignment of multiple protein structures based on sequence and structure features.
  Protein engineering, design & selection : PEDS 2009 Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A
• Insights into the molecular architecture of the 26S proteasome.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Nickell S, Beck F, Scheres SH, Korinek A, Förster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko JM, Carazo JM, Mann M, Baumeister W
• Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.
  Molecular & cellular proteomics : MCP 2009 DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT
• Evolutionary constraints on structural similarity in orthologs and paralogs.
  Protein science : a publication of the Protein Society 2009 Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A
• Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum.
  PloS one 2009 Pandey KC, Barkan DT, Sali A, Rosenthal PJ
• A kernel for open source drug discovery in tropical diseases.
  PLoS neglected tropical diseases 2009 Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA
• ModLink+: improving fold recognition by using protein-protein interactions.
  Bioinformatics (Oxford, England) 2009 Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B
• A kernel for the Tropical Disease Initiative.
  Nature biotechnology 2009 Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA
• Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.
  Journal of molecular biology 2009 Lasker K, Topf M, Sali A, Wolfson HJ
• Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
  Journal of structural and functional genomics 2009 Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, …
• The structural dynamics of macromolecular processes.
  Current opinion in cell biology 2009 Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A
• Outcome of a workshop on applications of protein models in biomedical research.
  Structure (London, England : 1993) 2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek…
• 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins.
  Journal of structural and functional genomics 2009 Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W
• Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.
  Journal of molecular biology 2008 Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM
• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.
  Journal of structural and functional genomics 2008 Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM
• MODBASE, a database of annotated comparative protein structure models and associated resources.
  Nucleic acids research 2008 Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A
• Genomic-scale prioritization of drug targets: the TDR Targets database.
  Nature reviews. Drug discovery 2008 Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington …
• How well can the accuracy of comparative protein structure models be predicted?
  Protein science : a publication of the Protein Society 2008 Eramian D, Eswar N, Shen MY, Sali A
• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
  Cell 2008 Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA
• Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
  PLoS computational biology 2008 Chiang RA, Sali A, Babbitt PC
• Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.
  Journal of molecular biology 2008 Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A
• Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W
• Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
  Nature structural & molecular biology 2008 Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J
• Prediction of enzyme function by combining sequence similarity and protein interactions.
  BMC bioinformatics 2008 Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B
• Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
  Structure (London, England : 1993) 2008 Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA
• Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios.
  Cancer informatics 2008 Karchin R, Agarwal M, Sali A, Couch F, Beattie MS
• Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure (London, England : 1993) 2008 Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW
• Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.
  Genes & development 2008 Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, Blackburn EH
• Protein production and purification.
  Nature methods 2008 Structural Genomics Consortium, China Structural Genomics Consortium, Northeast Structural Genomics Consortium, Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U,…
• Protein structure fitting and refinement guided by cryo-EM density.
  Structure (London, England : 1993) 2008 Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A
• Integrating diverse data for structure determination of macromolecular assemblies.
  Annual review of biochemistry 2008 Alber F, Förster F, Korkin D, Topf M, Sali A
• Protein structure modeling with MODELLER.
  Methods in molecular biology (Clifton, N.J.) 2008 Eswar N, Eramian D, Webb B, Shen MY, Sali A
• The molecular sociology of the cell.
  Nature 2007 Robinson CV, Sali A, Baumeister W
• Structural genomics of protein phosphatases.
  Journal of structural and functional genomics 2007 Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal…
• Stereochemical criteria for prediction of the effects of proline mutations on protein stability.
  PLoS computational biology 2007 Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R
• Determining the architectures of macromolecular assemblies.
  Nature 2007 Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A
• The molecular architecture of the nuclear pore complex.
  Nature 2007 Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP
• Comparative protein structure modeling using MODELLER.
  Current protocols in protein science 2007 Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A
• Structural genomics.
  Structure (London, England : 1993) 2007 Sali A, Lima CD, Kostic M
• Host pathogen protein interactions predicted by comparative modeling.
  Protein science : a publication of the Protein Society 2007 Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A
• Crystallographic conformers of actin in a biologically active bundle of filaments.
  Journal of molecular biology 2007 Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF
• Fold assessment for comparative protein structure modeling.
  Protein science : a publication of the Protein Society 2007 Melo F, Sali A
• Modeling mutations in protein structures.
  Protein science : a publication of the Protein Society 2007 Feyfant E, Sali A, Fiser A
• Characterization of protein hubs by inferring interacting motifs from protein interactions.
  PLoS computational biology 2007 Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B
• The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
  BMC bioinformatics 2007 Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A
• DBAli tools: mining the protein structure space.
  Nucleic acids research 2007 Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A
• The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family.
  Structure (London, England : 1993) 2007 Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH
• Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy.
  Epilepsia 2007 Soranzo N, Kelly L, Martinian L, Burley MW, Thom M, Sali A, Kroetz DL, Goldstein DB, Sisodiya SM
• Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.
  Cancer research 2007 Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, Goldgar D, Couch …
• Protein interactions and disease phenotypes in the ABC transporter superfamily.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007 Kelly L, Karchin R, Sali A
• Functional impact of missense variants in BRCA1 predicted by supervised learning.
  PLoS computational biology 2006 Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A
• Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term.
  Endocrinology 2006 Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ
• Statistical potential for assessment and prediction of protein structures.
  Protein science : a publication of the Protein Society 2006 Shen MY, Sali A
• Structural modeling of protein interactions by analogy: application to PSD-95.
  PLoS computational biology 2006 Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A
• Comparative protein structure modeling using Modeller.
  Current protocols in bioinformatics 2006 Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A
• Localization of binding sites in protein structures by optimization of a composite scoring function.
  Protein science : a publication of the Protein Society 2006 Rossi A, Marti-Renom MA, Sali A
• Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
  Journal of molecular biology 2006 Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF
• Outcome of a workshop on archiving structural models of biological macromolecules.
  Structure (London, England : 1993) 2006 Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, …
• A composite score for predicting errors in protein structure models.
  Protein science : a publication of the Protein Society 2006 Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA
• Protein complex compositions predicted by structural similarity.
  Nucleic acids research 2006 Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS
• Protease accessibility laddering: a proteomic tool for probing protein structure.
  Structure (London, England : 1993) 2006 Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP
• PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network.
  Pharmacological reviews 2006 Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL
• Simple fold composition and modular architecture of the nuclear pore complex.
  Proceedings of the National Academy of Sciences of the United States of America 2006 Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A
• Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.
  Journal of molecular biology 2006 Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A
• Variable gap penalty for protein sequence-structure alignment.
  Protein engineering, design & selection : PEDS 2006 Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A
• MODBASE: a database of annotated comparative protein structure models and associated resources.
  Nucleic acids research 2006 Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A
• Combining electron microscopy and comparative protein structure modeling.
  Current opinion in structural biology 2005 Topf M, Sali A
• The C-type lectin fold as an evolutionary solution for massive sequence variation.
  Nature structural & molecular biology 2005 McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P
• Localization of protein-binding sites within families of proteins.
  Protein science : a publication of the Protein Society 2005 Korkin D, Davis FP, Sali A
• Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition.
  International journal for parasitology 2005 Dvorák J, Delcroix M, Rossi A, Vopálenský V, Pospísek M, Sedinová M, Mikes L, Sajid M, Sali A, McKerrow JH, Horák P, Caffrey CR
• Detecting remotely related proteins by their interactions and sequence similarity.
  Proceedings of the National Academy of Sciences of the United States of America 2005 Espadaler J, Aragüés R, Eswar N, Marti-Renom MA, Querol E, Avilés FX, Sali A, Oliva B
• LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
  Bioinformatics (Oxford, England) 2005 Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A
• Structural characterization of assemblies from overall shape and subcomplex compositions.
  Structure (London, England : 1993) 2005 Alber F, Kim MF, Sali A
• Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22.
  Blood 2005 Yasuda S, Morokawa N, Wong GW, Rossi A, Madhusudhan MS, Sali A, Askew YS, Adachi R, Silverman GA, Krilis SA, Stevens RL
• Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.
  Journal of structural biology 2005 Topf M, Baker ML, John B, Chiu W, Sali A
• PIBASE: a comprehensive database of structurally defined protein interfaces.
  Bioinformatics (Oxford, England) 2005 Davis FP, Sali A
• Improving functional annotation of non-synonomous SNPs with information theory.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Karchin R, Kelly L, Sali A
• New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
  Journal of structural and functional genomics 2005 Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR,…
• Finding cures for tropical diseases: is open source an answer?
  PLoS medicine 2004 Maurer SM, Rai A, Sali A
• Components of coated vesicles and nuclear pore complexes share a common molecular architecture.
  PLoS biology 2004 Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP
• High-throughput computational and experimental techniques in structural genomics.
  Genome research 2004 Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N
• A structural perspective on protein-protein interactions.
  Current opinion in structural biology 2004 Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A
• Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.
  Cancer research 2004 Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN
• Comprehensive search for cysteine cathepsins in the human genome.
  Biological chemistry 2004 Rossi A, Deveraux Q, Turk B, Sali A
• Alignment of protein sequences by their profiles.
  Protein science : a publication of the Protein Society 2004 Marti-Renom MA, Madhusudhan MS, Sali A
• Detection of homologous proteins by an intermediate sequence search.
  Protein science : a publication of the Protein Society 2004 John B, Sali A
• MODBASE, a database of annotated comparative protein structure models, and associated resources.
  Nucleic acids research 2004 Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A
• ModLoop: automated modeling of loops in protein structures.
  Bioinformatics (Oxford, England) 2003 Fiser A, Sali A
• NIH workshop on structural proteomics of biological complexes.
  Structure (London, England : 1993) 2003 Sali A
• Comparative protein structure modeling by iterative alignment, model building and model assessment.
  Nucleic acids research 2003 John B, Sali A
• EVA: Evaluation of protein structure prediction servers.
  Nucleic acids research 2003 Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B
• Tools for comparative protein structure modeling and analysis.
  Nucleic acids research 2003 Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A
• Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
  Cell 2003 Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J
• The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons.
  Development (Cambridge, England) 2003 Lee SA, Shen EL, Fiser A, Sali A, Guo S
• From words to literature in structural proteomics.
  Nature 2003 Sali A, Glaeser R, Earnest T, Baumeister W
• ModView, visualization of multiple protein sequences and structures.
  Bioinformatics (Oxford, England) 2003 Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A
• Modeller: generation and refinement of homology-based protein structure models.
  Methods in enzymology 2003 Fiser A, Sali A
• Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies.
  Journal of immunology (Baltimore, Md. : 1950) 2002 Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang YX, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD
• Structural genomics: a pipeline for providing structures for the biologist.
  Protein science : a publication of the Protein Society 2002 Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK
• Reliability of assessment of protein structure prediction methods.
  Structure (London, England : 1993) 2002 Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A
• Statistical potentials for fold assessment.
  Protein science : a publication of the Protein Society 2002 Melo F, Sánchez R, Sali A
• MODBASE, a database of annotated comparative protein structure models.
  Nucleic acids research 2002 Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A