Andrej Sali

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 6

Top Topics

Protein Data Bank

Artificial Intelligence

Machine Learning

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

J. Chem. Inf. Model.

Publications

Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg V. Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben M. Webb, John D. Westbrook, Shamara Whetstone, Jasmine Young, Arthur O. Zalevsky, Christine Zardecki
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 Res. 51 (D1) (2023)
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva
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 Res. 49 (Database-Issue) (2021)
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, Ignacia Echeverria, Manjunatha Shivaraju, Azraa S. Chaudhury, Junjie Wang, Rosemary Williams, Jay R. Unruh, Charles H. Greenberg, Erica Y. Jacobs, Zhiheng Yu, M. Jason de la Cruz, Roxana Mironska, David L. Stokes, John D. Aitchison, Martin F. Jarrold, Jennifer L. Gerton, Steven J. Ludtke, Christopher W. Akey, Brian T. Chait, Andrej Sali, Michael P. Rout
Integrative structure and functional anatomy of a nuclear pore complex. Nat. 555 (7697) (2018)
Natalia Khuri, Arik A. Zur, Matthias B. Wittwer, Lawrence Lin, Sook Wah Yee, Andrej Sali, Kathleen M. Giacomini
Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1. J. Chem. Inf. Model. 57 (6) (2017)
Dina Schneidman-Duhovny, Michal Hammel, John A. Tainer, Andrej Sali
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
David T. Barkan, Xiao-li Cheng, Herodion Celino, Tran Trung Tran, Ashok Bhandari, Charles S. Craik, Andrej Sali, Mark L. Smythe
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinform. 17 (2016)
Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrão
Oocytes. PLoS Comput. Biol. 11 (8) (2015)
Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis. PLoS Comput. Biol. 10 (12) (2014)
Guang Qiang Dong, Sara Calhoun, Hao Fan, Chakrapani Kalyanaraman, Megan C. Branch, Susan T. Mashiyama, Nir London, Matthew P. Jacobson, Patricia C. Babbitt, Brian K. Shoichet, Richard N. Armstrong, Andrej Sali
Prediction of Substrates for Glutathione Transferases by Covalent Docking. J. Chem. Inf. Model. 54 (6) (2014)
Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali
ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 42 (Database-Issue) (2014)
Guang Qiang Dong, Hao Fan, Dina Schneidman-Duhovny, Ben M. Webb, Andrej Sali
Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinform. 29 (24) (2013)
Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain M. Wallace, Vinod Kumar, Ursula Pieper, Andrej Sali, James R. Brown, John P. Overington, Marc A. Martí-Renom
. PLoS Comput. Biol. 9 (10) (2013)
Hannes Braberg, Benjamin M. Webb, Elina Tjioe, Ursula Pieper, Andrej Sali, Mallur S. Madhusudhan
SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinform. 28 (15) (2012)
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, Shoshannah L. Roth, Eyal Akiva, John Marlett, Melanie Stephens, Iván D'Orso, Jason Fernandes, Marie E. Fahey, Cathal Mahon, Anthony J. O'Donoghue, Aleksandar Todorovic, John H. Morris, David A. Maltby, Tom Alber, Gerard Cagney, Frederic D. Bushman, John A. Young, Sumit K. Chanda, Wesley I. Sundquist, Tanja Kortemme, Ryan D. Hernandez, Charles S. Craik, Alma Burlingame, Andrej Sali, Alan D. Frankel, Nevan J. Krogan
Global landscape of HIV-human protein complexes. Nat. 481 (7381) (2012)
Dina Schneidman-Duhovny, Andrea Rossi, 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, Arvind Rajpal, Jaume Pons, David A. Agard, Yifan Cheng, Andrej Sali
A method for integrative structure determination of protein-protein complexes. Bioinform. 28 (24) (2012)
Hao Fan, Dina Schneidman-Duhovny, John J. Irwin, Guang Qiang Dong, Brian K. Shoichet, Andrej Sali
Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions. J. Chem. Inf. Model. 51 (12) (2011)
Ursula Pieper, 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, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39 (Database-Issue) (2011)
Elina Tjioe, Keren Lasker, Ben M. Webb, Haim J. Wolfson, Andrej Sali
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
David T. Barkan, Daniel R. Hostetter, Sami Mahrus, Ursula Pieper, James A. Wells, Charles S. Craik, Andrej Sali
Prediction of protease substrates using sequence and structure features. Bioinform. 26 (14) (2010)
Fred P. Davis, Andrej Sali
The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures. PLoS Comput. Biol. 6 (2) (2010)
Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali
FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Ursula Pieper, 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
MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 37 (Database-Issue) (2009)
Timothy R. Lezon, Andrej Sali, Ivet Bahar
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. PLoS Comput. Biol. 5 (9) (2009)
Oriol Fornes, Ramon Aragues, Jordi Espadaler, Marc A. Martí-Renom, Andrej Sali, Baldo Oliva
ModLink+: improving fold recognition by using protein-protein interactions. Bioinform. 25 (12) (2009)
Hao Fan, John J. Irwin, Benjamin M. Webb, Gerhard Klebe, Brian K. Shoichet, Andrej Sali
Molecular Docking Screens Using Comparative Models of Proteins. J. Chem. Inf. Model. 49 (11) (2009)
Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Comput. Biol. 4 (8) (2008)
Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X. Avilés, Andrej Sali, Marc A. Martí-Renom, Baldomero Oliva
Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinform. 9 (2008)
Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Comput. Biol. 3 (2) (2007)
Marc A. Martí-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinform. 8 (S-4) (2007)
Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Martí-Renom, Baldo Oliva
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. PLoS Comput. Biol. 3 (9) (2007)
Libusha Kelly, Rachel Karchin, Andrej Sali
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. Pacific Symposium on Biocomputing (2007)
Kanika Bajaj, Mallur S. Madhusudhan, Bharat V. Adkar, Purbani Chakrabarti, C. Ramakrishnan, Andrej Sali, Raghavan Varadarajan
Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability. PLoS Comput. Biol. 3 (12) (2007)
Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali
DBAli tools: mining the protein structure space. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur S. Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali
MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34 (Database-Issue) (2006)
Dmitry Korkin, Fred P. Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, Mary B. Kennedy, Andrej Sali
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. PLoS Comput. Biol. 2 (11) (2006)
Fred P. Davis, Andrej Sali
PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinform. 21 (9) (2005)
Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinform. 21 (12) (2005)
Rachel Karchin, Libusha Kelly, Andrej Sali
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. Pacific Symposium on Biocomputing (2005)
Ursula Pieper, Narayanan Eswar, Hannes Braberg, Mallur S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Martí-Renom, András Fiser, Ben M. Webb, Daniel M. Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32 (Database-Issue) (2004)
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
EVA: evaluation of protein structure prediction servers. Nucleic Acids Res. 31 (13) (2003)
Narayanan Eswar, Bino John, Nebojsa Mirkovic, András Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Mallur S. Madhusudhan, Bozidar Yerkovich, Andrej Sali
Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 31 (13) (2003)
András Fiser, Andrej Sali
ModLoop: automated modeling of loops in protein structures. Bioinform. 19 (18) (2003)
Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali
ModView, visualization of multiple protein sequences and structures. Bioinform. 19 (1) (2003)
Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30 (1) (2002)
Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinform. 18 (1) (2002)
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. 17 (10) (2001)
Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali
DBAli: a database of protein structure alignments. Bioinform. 17 (8) (2001)
Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
EVA: continuous automatic evaluation of protein structure prediction servers. Bioinform. 17 (12) (2001)
Roberto Sánchez, Ursula Pieper, Nebojsa Mirkovic, Paul I. W. de Bakker, Edward Wittenstein, Andrej Sali
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 28 (1) (2000)
Chris Burge, Andrej Sali, Mark Borodovsky
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA). Bioinform. 15 (11) (1999)
Andrej Sali, Eugene I. Shakhnovich, Martin Karplus
Thermodynamics and kinetics of protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding (1995)