Andrej Sali

53 papers Misc 2Journal 49Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.
Bioinform.
Thomas-Otavio Peulen, Katherina Hemmen, Annemarie Greife, Benjamin M. Webb, Suren Felekyan, Andrej Sali, Claus A. M. Seidel, Hugo Sanabria, Katrin G. Heinze
2023 J jnl
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.
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
2021 J jnl
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.
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
2018 J jnl
Integrative structure and functional anatomy of a nuclear pore complex.
Nat.
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
2017 J jnl
Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1.
J. Chem. Inf. Model.
Natalia Khuri, Arik A. Zur, Matthias B. Wittwer, Lawrence Lin, Sook Wah Yee, Andrej Sali, Kathleen M. Giacomini
2016 J jnl
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23.
BMC Bioinform.
David T. Barkan, Xiao-li Cheng, Herodion Celino, Tran Trung Tran, Ashok Bhandari, Charles S. Craik, Andrej Sali, Mark L. Smythe
2016 J jnl
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.
Nucleic Acids Res.
Dina Schneidman-Duhovny, Michal Hammel, John A. Tainer, Andrej Sali
2015 J jnl
Prediction of Functionally Important Phospho-Regulatory Events in
PLoS Comput. Biol.
Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrão
2014 J jnl
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis.
PLoS Comput. Biol.
Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach
2014 J jnl
ModBase, a database of annotated comparative protein structure models and associated resources.
Nucleic Acids Res.
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
2014 J jnl
Prediction of Substrates for Glutathione Transferases by Covalent Docking.
J. Chem. Inf. Model.
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
2013 J jnl
Optimized atomic statistical potentials: assessment of protein interfaces and loops.
Bioinform.
Guang Qiang Dong, Hao Fan, Dina Schneidman-Duhovny, Ben M. Webb, Andrej Sali
2013 J jnl
Target Prediction for an Open Access Set of Compounds Active against
PLoS Comput. Biol.
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
2012 J jnl
A method for integrative structure determination of protein-protein complexes.
Bioinform.
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
2012 J jnl
Global landscape of HIV-human protein complexes.
Nat.
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
2012 J jnl
SALIGN: a web server for alignment of multiple protein sequences and structures.
Bioinform.
Hannes Braberg, Benjamin M. Webb, Elina Tjioe, Ursula Pieper, Andrej Sali, Mallur S. Madhusudhan
2011 J jnl
ModBase, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res.
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
2011 J jnl
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.
Nucleic Acids Res.
Elina Tjioe, Keren Lasker, Ben M. Webb, Haim J. Wolfson, Andrej Sali
2011 J jnl
Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions.
J. Chem. Inf. Model.
Hao Fan, Dina Schneidman-Duhovny, John J. Irwin, Guang Qiang Dong, Brian K. Shoichet, Andrej Sali
2010 J jnl
FoXS: a web server for rapid computation and fitting of SAXS profiles.
Nucleic Acids Res.
Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali
2010 J jnl
Prediction of protease substrates using sequence and structure features.
Bioinform.
David T. Barkan, Daniel R. Hostetter, Sami Mahrus, Ursula Pieper, James A. Wells, Charles S. Craik, Andrej Sali
2010 J jnl
The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures.
PLoS Comput. Biol.
Fred P. Davis, Andrej Sali
2009 J jnl
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models.
PLoS Comput. Biol.
Timothy R. Lezon, Andrej Sali, Ivet Bahar
2009 J jnl
MODBASE, a database of annotated comparative protein structure models and associated resources.
Nucleic Acids Res.
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
2009 J jnl
ModLink+: improving fold recognition by using protein-protein interactions.
Bioinform.
Oriol Fornes, Ramon Aragues, Jordi Espadaler, Marc A. Martí-Renom, Andrej Sali, Baldo Oliva
2009 J jnl
Molecular Docking Screens Using Comparative Models of Proteins.
J. Chem. Inf. Model.
Hao Fan, John J. Irwin, Benjamin M. Webb, Gerhard Klebe, Brian K. Shoichet, Andrej Sali
2008 J jnl
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies.
PLoS Comput. Biol.
Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt
2008 — ch.
Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints.
Protein-protein Interactions and Networks
Frank Alber, Brian T. Chait, Michael P. Rout, Andrej Sali
2008 J jnl
Prediction of enzyme function by combining sequence similarity and protein interactions.
BMC Bioinform.
Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X. Avilés, Andrej Sali, Marc A. Martí-Renom, Baldomero Oliva
2007 J jnl
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions.
PLoS Comput. Biol.
Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Martí-Renom, Baldo Oliva
2007 J jnl
DBAli tools: mining the protein structure space.
Nucleic Acids Res.
Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali
2007 J jnl
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning.
PLoS Comput. Biol.
Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
2007 Misc conf
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily.
Pacific Symposium on Biocomputing
Libusha Kelly, Rachel Karchin, Andrej Sali
2007 J jnl
Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability.
PLoS Comput. Biol.
Kanika Bajaj, Mallur S. Madhusudhan, Bharat V. Adkar, Purbani Chakrabarti, C. Ramakrishnan, Andrej Sali, Raghavan Varadarajan
2007 J jnl
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC Bioinform.
Marc A. Martí-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2006 J jnl
MODBASE: a database of annotated comparative protein structure models and associated resources.
Nucleic Acids Res.
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
2006 J jnl
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95.
PLoS Comput. Biol.
Dmitry Korkin, Fred P. Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, Mary B. Kennedy, Andrej Sali
2005 Misc conf
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory.
Pacific Symposium on Biocomputing
Rachel Karchin, Libusha Kelly, Andrej Sali
2005 J jnl
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Bioinform.
Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali
2005 J jnl
PIBASE: a comprehensive database of structurally defined protein interfaces.
Bioinform.
Fred P. Davis, Andrej Sali
2004 J jnl
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res.
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
2003 J jnl
EVA: evaluation of protein structure prediction servers.
Nucleic Acids Res.
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
2003 J jnl
ModLoop: automated modeling of loops in protein structures.
Bioinform.
András Fiser, Andrej Sali
2003 J jnl
ModView, visualization of multiple protein sequences and structures.
Bioinform.
Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali
2003 J jnl
Tools for comparative protein structure modeling and analysis.
Nucleic Acids Res.
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
2002 J jnl
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.
Bioinform.
Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali
2002 J jnl
MODBASE, a database of annotated comparative protein structure models.
Nucleic Acids Res.
Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali
2001 J jnl
DBAli: a database of protein structure alignments.
Bioinform.
Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali
2001 J jnl
EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinform.
Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
2001 J jnl
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).
Bioinform.
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
2000 J jnl
MODBASE, a database of annotated comparative protein structure models.
Nucleic Acids Res.
Roberto Sánchez, Ursula Pieper, Nebojsa Mirkovic, Paul I. W. de Bakker, Edward Wittenstein, Andrej Sali
1999 J jnl
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA).
Bioinform.
Chris Burge, Andrej Sali, Mark Borodovsky
1995 — conf
Thermodynamics and kinetics of protein folding.
Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding
Andrej Sali, Eugene I. Shakhnovich, Martin Karplus