Andrej Sali

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. Bioinformatics 28(15): 2072-2073 (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. Bioinformatics 28(24): 3282-3289 (2012)

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 Research 39(Database-Issue): 465-474 (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 Research 39(Web-Server-Issue): 167-170 (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. Bioinformatics 26(14): 1714-1722 (2010)

Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali: FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Research 38(Web-Server-Issue): 540-544 (2010)

Fred P. Davis, Andrej Sali: The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures. PLoS Computational Biology 6(2) (2010)

Oriol Fornes, Ramon Aragues, Jordi Espadaler, Marc A. Martí-Renom, Andrej Sali, Baldo Oliva: ModLink+: improving fold recognition by using protein-protein interactions. Bioinformatics 25(12): 1506-1512 (2009)

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 Research 37(Database-Issue): 347-354 (2009)

Timothy R. Lezon, Andrej Sali, Ivet Bahar: Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. PLoS Computational Biology 5(9) (2009)

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 Bioinformatics 9 (2008)

Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt: Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Computational Biology 4(8) (2008)

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 Bioinformatics 8(S-4) (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 Research 35(Web-Server-Issue): 393-397 (2007)

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 Computational Biology 3(2) (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 Computational Biology 3(9) (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 Computational Biology 3(12) (2007)

Libusha Kelly, Rachel Karchin, Andrej Sali: Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. Pacific Symposium on Biocomputing 2007: 51-63

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 Research 34(Database-Issue): 291-295 (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 Computational Biology 2(11) (2006)

Fred P. Davis, Andrej Sali: PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21(9): 1901-1907 (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. Bioinformatics 21(12): 2814-2820 (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 Research 32(Database-Issue): 217-222 (2004)

Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali: ModView, visualization of multiple protein sequences and structures. Bioinformatics 19(1): 165-166 (2003)

András Fiser, Andrej Sali: ModLoop: automated modeling of loops in protein structures. Bioinformatics 19(18): 2500-2501 (2003)

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 Research 31(13): 3311-3315 (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 Research 31(13): 3375-3380 (2003)

Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali: LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18(1): 200-201 (2002)

Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali: MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30(1): 255-259 (2002)

Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali: DBAli: a database of protein structure alignments. Bioinformatics 17(8): 746-747 (2001)

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). Bioinformatics 17(10): 859-861 (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. Bioinformatics 17(12): 1242-1243 (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 Research 28(1): 250-253 (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). Bioinformatics 15(11): 865-866 (1999)