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ORCIDAndrej Sali
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2020 – today
- 2023
[j48]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): 488-508 (2023)- 2021
- [j47]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): D437-D451 (2021)
2010 – 2019
- 2018
- [j46]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): 475-482 (2018) - 2017
- [j45]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): 1402-1413 (2017) - 2016
- [j44]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: 481:1-481:16 (2016) - [j43]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): W424-W429 (2016) - 2015
- [j42]Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrão:
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput. Biol. 11(8) (2015) - 2014
- [j41]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): 1687-1699 (2014) - [j40]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): 336-346 (2014) - [j39]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) - 2013
- [j38]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): 3158-3166 (2013) - [j37]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:
Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis. PLoS Comput. Biol. 9(10) (2013) - 2012
- [j36]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): 2072-2073 (2012) - [j35]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): 3282-3289 (2012) - [j34]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): 365-370 (2012) - 2011
- [j33]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): 3078-3092 (2011) - [j32]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): 465-474 (2011) - [j31]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): 167-170 (2011) - 2010
- [j30]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): 1714-1722 (2010) - [j29]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): 540-544 (2010) - [j28]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)
2000 – 2009
- 2009
- [j27]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): 1506-1512 (2009) - [j26]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): 2512-2527 (2009) - [j25]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): 347-354 (2009) - [j24]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) - 2008
- [j23]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) - [j22]Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt:
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Comput. Biol. 4(8) (2008) - [p1]Frank Alber, Brian T. Chait, Michael P. Rout, Andrej Sali:
Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. Protein-protein Interactions and Networks 2008: 99-114 - 2007
- [j21]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) - [j20]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): 393-397 (2007) - [j19]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) - [j18]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) - [j17]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) - [c3]Libusha Kelly, Rachel Karchin, Andrej Sali:
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. Pacific Symposium on Biocomputing 2007: 51-63 - 2006
- [j16]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): 291-295 (2006) - [j15]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) - 2005
- [j14]Fred P. Davis, Andrej Sali:
PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinform. 21(9): 1901-1907 (2005) - [j13]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): 2814-2820 (2005) - [c2]Rachel Karchin, Libusha Kelly, Andrej Sali:
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. Pacific Symposium on Biocomputing 2005 - 2004
- [j12]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): 217-222 (2004) - 2003
- [j11]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): 165-166 (2003) - [j10]András Fiser, Andrej Sali:
ModLoop: automated modeling of loops in protein structures. Bioinform. 19(18): 2500-2501 (2003) - [j9]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): 3311-3315 (2003) - [j8]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): 3375-3380 (2003) - 2002
- [j7]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): 200-201 (2002) - [j6]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): 255-259 (2002) - 2001
- [j5]Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali:
DBAli: a database of protein structure alignments. Bioinform. 17(8): 746-747 (2001) - [j4]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): 859-861 (2001) - [j3]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): 1242-1243 (2001) - 2000
- [j2]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): 250-253 (2000)
1990 – 1999
- 1999
- [j1]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): 865-866 (1999) - 1995
- [c1]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: 199-213
Coauthor Index
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