Thermodynamics and kinetics of protein folding. - Andrej Sali; Eugene I. Shakhnovich; Martin Karplus (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA). - Chris Burge; Andrej Sali; Mark Borodovsky (Bioinform., 1999)

MODBASE, a database of annotated comparative protein structure models. - Roberto Sánchez; Ursula Pieper 001; Nebojsa Mirkovic; Paul I. W. de Bakker; Edward Wittenstein; Andrej Sali (Nucleic Acids Res., 2000)

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). - Mark Borodovsky; Eugene V. Koonin; Chris Burge; James W. Fickett; John Logsdon; Andrej Sali; Gary D. Stormo; Igor B. Zhulin (Bioinform., 2001)

EVA: continuous automatic evaluation of protein structure prediction servers. - Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; András Fiser; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Bioinform., 2001)

DBAli: a database of protein structure alignments. - Marc A. Martí-Renom; Valentin A. Ilyin; Andrej Sali (Bioinform., 2001)

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. - Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali (Bioinform., 2002)

MODBASE, a database of annotated comparative protein structure models. - Ursula Pieper 001; Narayanan Eswar; Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali (Nucleic Acids Res., 2002)

ModLoop: automated modeling of loops in protein structures. - András Fiser; Andrej Sali (Bioinform., 2003)

ModView, visualization of multiple protein sequences and structures. - Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Linda McMahan; Andrej Sali (Bioinform., 2003)

Tools for comparative protein structure modeling and analysis. - Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Mallur S. Madhusudhan; Bozidar Yerkovich; Andrej Sali (Nucleic Acids Res., 2003)

EVA: evaluation of protein structure prediction servers. - Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Nucleic Acids Res., 2003)

MODBASE, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Narayanan Eswar; Hannes Braberg; Mallur S. Madhusudhan; Fred P. Davis; Ashley C. Stuart; Nebojsa Mirkovic; Andrea Rossi 005; Marc A. Martí-Renom; András Fiser; Ben M. Webb; Daniel M. Greenblatt; et al. (Nucleic Acids Res., 2004)

Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. - Rachel Karchin; Libusha Kelly; Andrej Sali (Pacific Symposium on Biocomputing, 2005)

PIBASE: a comprehensive database of structurally defined protein interfaces. - Fred P. Davis; Andrej Sali (Bioinform., 2005)

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. - Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J. Thomas; Ursula Pieper 001; Narayanan Eswar; David Haussler; Andrej Sali (Bioinform., 2005)

MODBASE: a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Fred P. Davis; Hannes Braberg; Mallur S. Madhusudhan; Andrea Rossi 005; Marc A. Martí-Renom; Rachel Karchin; Ben M. Webb; David Eramian; Min-Yi Shen; Libusha Kelly; et al. (Nucleic Acids Res., 2006)

Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. - Dmitry Korkin; Fred P. Davis; Frank Alber; Tinh Luong; Min-Yi Shen; Vladan Lucic; Mary B. Kennedy; Andrej Sali (PLoS Comput. Biol., 2006)

Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. - Libusha Kelly; Rachel Karchin; Andrej Sali (Pacific Symposium on Biocomputing, 2007)

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. - Marc A. Martí-Renom; Andrea Rossi 005; Fátima Al-Shahrour; Fred P. Davis; Ursula Pieper 001; Joaquín Dopazo; Andrej Sali (BMC Bioinform., 2007)

DBAli tools: mining the protein structure space. - Marc A. Martí-Renom; Ursula Pieper 001; Mallur S. Madhusudhan; Andrea Rossi 005; Narayanan Eswar; Fred P. Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali (Nucleic Acids Res., 2007)

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. - Ramon Aragues; Andrej Sali; Jaume Bonet; Marc A. Martí-Renom; Baldo Oliva (PLoS Comput. Biol., 2007)

Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability. - Kanika Bajaj; Mallur S. Madhusudhan; Bharat V. Adkar; Purbani Chakrabarti; C. Ramakrishnan; Andrej Sali; Raghavan Varadarajan (PLoS Comput. Biol., 2007)

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. - Rachel Karchin; Alvaro N. A. Monteiro; Sean V. Tavtigian; Marcelo A. Carvalho; Andrej Sali (PLoS Comput. Biol., 2007)

Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. - Frank Alber; Brian T. Chait; Michael P. Rout; Andrej Sali (Protein-protein Interactions and Networks, 2008)

Prediction of enzyme function by combining sequence similarity and protein interactions. - Jordi Espadaler; Narayanan Eswar; Enrique Querol; Francesc X. Avilés; Andrej Sali; Marc A. Martí-Renom; Baldomero Oliva (BMC Bioinform., 2008)

Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. - Ranyee A. Chiang; Andrej Sali; Patricia C. Babbitt (PLoS Comput. Biol., 2008)

ModLink+: improving fold recognition by using protein-protein interactions. - Oriol Fornes; Ramon Aragues; Jordi Espadaler; Marc A. Martí-Renom; Andrej Sali; Baldo Oliva (Bioinform., 2009)

Molecular Docking Screens Using Comparative Models of Proteins. - Hao Fan 002; John J. Irwin; Benjamin M. Webb; Gerhard Klebe; Brian K. Shoichet; Andrej Sali (J. Chem. Inf. Model., 2009)

MODBASE, a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Ben M. Webb; David Eramian; Libusha Kelly; David T. Barkan; Hannah Carter; Parminder Mankoo; Rachel Karchin; Marc A. Martí-Renom; Fred P. Davis; Andrej Sali (Nucleic Acids Res., 2009)

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. - Timothy R. Lezon; Andrej Sali; Ivet Bahar (PLoS Comput. Biol., 2009)

Prediction of protease substrates using sequence and structure features. - David T. Barkan; Daniel R. Hostetter; Sami Mahrus; Ursula Pieper 001; James A. Wells; Charles S. Craik; Andrej Sali (Bioinform., 2010)

FoXS: a web server for rapid computation and fitting of SAXS profiles. - Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali (Nucleic Acids Res., 2010)

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures. - Fred P. Davis; Andrej Sali (PLoS Comput. Biol., 2010)

Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions. - Hao Fan 002; Dina Schneidman-Duhovny; John J. Irwin; Guang Qiang Dong; Brian K. Shoichet; Andrej Sali (J. Chem. Inf. Model., 2011)

ModBase, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Benjamin M. Webb; David T. Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C. Meng; Eric F. Pettersen; Conrad C. Huang; Ruchira S. Datta; Parthasarathy Sampathkumar; et al. (Nucleic Acids Res., 2011)

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. - Elina Tjioe; Keren Lasker; Ben M. Webb; Haim J. Wolfson; Andrej Sali (Nucleic Acids Res., 2011)

SALIGN: a web server for alignment of multiple protein sequences and structures. - Hannes Braberg; Benjamin M. Webb; Elina Tjioe; Ursula Pieper 001; Andrej Sali; Mallur S. Madhusudhan (Bioinform., 2012)

A method for integrative structure determination of protein-protein complexes. - Dina Schneidman-Duhovny; Andrea Rossi 005; Agustin Avila-Sakar; Seung Joong Kim; Javier A. Velázquez-Muriel; Pavel Strop; Hong Liang; Kristin A. Krukenberg; Maofu Liao; Ho Min Kim; Solmaz Sobhanifar; Volker Dötsch; et al. (Bioinform., 2012)

Global landscape of HIV-human protein complexes. - Stefanie Jäger; Peter Cimermancic; Natali Gulbahce; Jeffrey R. Johnson; Kathryn E. McGovern; Starlynn C. Clarke; Michael Shales; Gaelle Mercenne; Lars Pache; Kathy Li; Hilda Hernandez; Gwendolyn M. Jang; et al. (Nat., 2012)

Optimized atomic statistical potentials: assessment of protein interfaces and loops. - Guang Qiang Dong; Hao Fan 002; Dina Schneidman-Duhovny; Ben M. Webb; Andrej Sali (Bioinform., 2013)

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis. - Francisco Martínez-Jiménez; George Papadatos; Lun Yang; Iain M. Wallace; Vinod Kumar; Ursula Pieper 001; Andrej Sali; James R. Brown; John P. Overington; Marc A. Martí-Renom (PLoS Comput. Biol., 2013)

Prediction of Substrates for Glutathione Transferases by Covalent Docking. - Guang Qiang Dong; Sara Calhoun; Hao Fan 002; Chakrapani Kalyanaraman; Megan C. Branch; Susan T. Mashiyama; Nir London; Matthew P. Jacobson; Patricia C. Babbitt; Brian K. Shoichet; Richard N. Armstrong; Andrej Sali (J. Chem. Inf. Model., 2014)

ModBase, a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Benjamin M. Webb; Guang Qiang Dong; Dina Schneidman-Duhovny; Hao Fan 002; Seung Joong Kim; Natalia Khuri; Yannick G. Spill; Patrick Weinkam; Michal Hammel; John A. Tainer; Michael Nilges; et al. (Nucleic Acids Res., 2014)

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis. - Marnix H. Medema; Peter Cimermancic; Andrej Sali; Eriko Takano; Michael A. Fischbach (PLoS Comput. Biol., 2014)

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. - Jeffrey R. Johnson; Silvia D. Santos; Tasha Johnson; Ursula Pieper 001; Marta Strumillo; Omar Wagih; Andrej Sali; Nevan J. Krogan; Pedro Beltrão (PLoS Comput. Biol., 2015)

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. - David T. Barkan; Xiao-li Cheng; Herodion Celino; Tran Trung Tran; Ashok Bhandari; Charles S. Craik; Andrej Sali; Mark L. Smythe (BMC Bioinform., 2016)

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. - Dina Schneidman-Duhovny; Michal Hammel; John A. Tainer; Andrej Sali (Nucleic Acids Res., 2016)

Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1. - Natalia Khuri; Arik A. Zur; Matthias B. Wittwer; Lawrence Lin; Sook Wah Yee; Andrej Sali; Kathleen M. Giacomini (J. Chem. Inf. Model., 2017)

Integrative structure and functional anatomy of a nuclear pore complex. - Seung Joong Kim; Javier Fernandez-Martinez; Ilona Nudelman; Yi Shi; Wenzhu Zhang; Barak Raveh; Thurston Herricks; Brian D. Slaughter; Joanna A. Hogan; Paula Upla; Ilan E. Chemmama; Riccardo Pellarin; et al. (Nat., 2018)

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. - Stephen K. Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen 022; Gregg V. Crichlow; Cole H. Christie; Kenneth Dalenberg; Luigi Di Costanzo; Jose M. Duarte; Shuchismita Dutta; Zukang Feng; et al. (Nucleic Acids Res., 2021)

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. - Stephen K. Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Henry Chao; Li Chen 022; Paul A. Craig; Gregg V. Crichlow; Kenneth Dalenberg; Jose M. Duarte; Shuchismita Dutta; Maryam Fayazi; et al. (Nucleic Acids Res., 2023)