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Donald S. Petrey, Ph.D. - Publications

Institution:
Columbia University, New York, NY
Area:
computational biophysics and bioinformatics
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zhao H, Murray D, Petrey D, Honig B. ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models. Research Square. PMID 37790387 DOI: 10.21203/rs.3.rs-3289791/v1  0.799
2023 Petrey D, Zhao H, Trudeau S, Murray D, Honig B. PrePPI: A structure informed proteome-wide database of protein-protein interactions. Journal of Molecular Biology. 168052. PMID 36933822 DOI: 10.1016/j.jmb.2023.168052  0.794
2023 Petrey D, Zhao H, Trudeau S, Murray D, Honig B. PrePPI: A structure informed proteome-wide database of protein-protein interactions. Biorxiv : the Preprint Server For Biology. PMID 36909476 DOI: 10.1101/2023.02.27.530276  0.794
2023 Trudeau SJ, Hwang H, Mathur D, Begum K, Petrey D, Murray D, Honig B. PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Protein Science : a Publication of the Protein Society. e4594. PMID 36776141 DOI: 10.1002/pro.4594  0.617
2021 Murray D, Petrey D, Honig B. Integrating 3D structural information into systems biology. The Journal of Biological Chemistry. 100562. PMID 33744294 DOI: 10.1016/j.jbc.2021.100562  0.603
2020 Ganapathi M, Argyriou L, Martínez-Azorín F, Morlot S, Yigit G, Lee TM, Auber B, von Gise A, Petrey DS, Thiele H, Cyganek L, Sabater-Molina M, Ahimaz P, Cabezas-Herrera J, Sorlí-García M, et al. Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Human Genetics. PMID 32514796 DOI: 10.1007/S00439-020-02188-6  0.553
2017 Hwang H, Dey F, Petrey D, Honig B. Structure-based prediction of ligand-protein interactions on a genome-wide scale. Proceedings of the National Academy of Sciences of the United States of America. PMID 29229851 DOI: 10.1073/Pnas.1705381114  0.677
2017 Lopez-Rivera E, Liu YP, Verbitsky M, Anderson BR, Capone VP, Otto EA, Yan Z, Mitrotti A, Martino J, Steers NJ, Fasel DA, Vukojevic K, Deng R, Racedo SE, Liu Q, ... ... Petrey DS, et al. Genetic Drivers of Kidney Defects in the DiGeorge Syndrome. The New England Journal of Medicine. PMID 28121514 DOI: 10.1056/Nejmoa1609009  0.459
2016 Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. A computational interactome and functional annotation for the human proteome. Elife. 5. PMID 27770567 DOI: 10.7554/Elife.18715  0.641
2016 Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. Author response: A computational interactome and functional annotation for the human proteome Elife. DOI: 10.7554/Elife.18715.074  0.489
2015 Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Science : a Publication of the Protein Society. PMID 26178156 DOI: 10.1002/Pro.2744  0.707
2015 Chen TS, Petrey D, Garzon JI, Honig B. Predicting peptide-mediated interactions on a genome-wide scale. Plos Computational Biology. 11: e1004248. PMID 25938916 DOI: 10.1371/Journal.Pcbi.1004248  0.669
2015 Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B. Template-based prediction of protein function. Current Opinion in Structural Biology. 32: 33-8. PMID 25678152 DOI: 10.1016/J.Sbi.2015.01.007  0.73
2015 Broyde J, Simpson D, Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov A, Lachmann A, Hill DE, Vidal M, Jackson P, Honig B, Sweet-Cordero A, Califano A. Abstract PR13: Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr13  0.569
2014 Petrey D, Honig B. Structural bioinformatics of the interactome Annual Review of Biophysics. 43: 193-210. PMID 24895853 DOI: 10.1146/Annurev-Biophys-051013-022726  0.584
2014 Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov T, Broyde J, Rieckhof GE, Honig B, Califano A. Abstract PR09: A systems biology approach to elucidate novel drug targets in KRAS mutant tumors Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Rasonc14-Pr09  0.485
2013 Dey F, Zhang QC, Petrey D, Honig B. Toward a "structural BLAST": Using structural relationships to infer function Protein Science. 22: 359-366. PMID 23349097 DOI: 10.1002/Pro.2225  0.792
2013 Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Research. 41: D828-33. PMID 23193263 DOI: 10.1093/Nar/Gks1231  0.75
2013 Zhang QC, Petrey D, Honig B. 180 Integrating structural and systems biology: structure-based prediction of protein–protein interactions on a genome-wide scale Journal of Biomolecular Structure and Dynamics. 31: 116-116. DOI: 10.1080/07391102.2013.786422  0.779
2013 Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Correction: Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale Nature. 495: 127-127. DOI: 10.1038/Nature11977  0.704
2012 Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 490: 556-60. PMID 23023127 DOI: 10.1038/Nature11503  0.78
2012 Aramini JM, Petrey D, Lee DY, Janjua H, Xiao R, Acton TB, Everett JK, Montelione GT. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. Journal of Structural and Functional Genomics. 13: 171-6. PMID 22592539 DOI: 10.1007/S10969-012-9135-5  0.467
2012 Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. Journal of Structural and Functional Genomics. 13: 1-7. PMID 22223187 DOI: 10.1007/S10969-011-9121-3  0.712
2011 Kuziemko A, Honig B, Petrey D. Using structure to explore the sequence alignment space of remote homologs. Plos Computational Biology. 7: e1002175. PMID 21998567 DOI: 10.1371/Journal.Pcbi.1002175  0.688
2011 Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Research. 39: W357-61. PMID 21672961 DOI: 10.1093/Nar/Gkr468  0.729
2011 Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Research. 39: W283-7. PMID 21609948 DOI: 10.1093/Nar/Gkr311  0.739
2010 Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proceedings of the National Academy of Sciences of the United States of America. 107: 10896-901. PMID 20534496 DOI: 10.1073/Pnas.1005894107  0.771
2010 Norel R, Petrey D, Honig B. PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Research. 38: W550-4. PMID 20525783 DOI: 10.1093/Nar/Gkq475  0.65
2010 Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. Journal of Structural and Functional Genomics. 11: 51-9. PMID 20383749 DOI: 10.1007/S10969-010-9086-7  0.699
2009 Petrey D, Fischer M, Honig B. Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proceedings of the National Academy of Sciences of the United States of America. 106: 17377-82. PMID 19805138 DOI: 10.1073/Pnas.0907971106  0.663
2009 Petrey D, Honig B. Is protein classification necessary? Toward alternative approaches to function annotation Current Opinion in Structural Biology. 19: 363-368. PMID 19269161 DOI: 10.1016/J.Sbi.2009.02.001  0.683
2008 Norel R, Sheinerman F, Petrey D, Honig B. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Science. 10: 2147-2161. PMID 11604522 DOI: 10.1110/Ps.12901  0.551
2006 Kolodny R, Petrey D, Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Current Opinion in Structural Biology. 16: 393-8. PMID 16678402 DOI: 10.1016/J.Sbi.2006.04.007  0.687
2005 Petrey D, Honig B. Protein structure prediction: Inroads to biology Molecular Cell. 20: 811-819. PMID 16364908 DOI: 10.1016/J.Molcel.2005.12.005  0.708
2004 Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B. Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Research. 32: 2566-77. PMID 15141026 DOI: 10.1093/Nar/Gkh580  0.513
2003 Petrey D, Honig B. GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences Methods in Enzymology. 374: 492-509. PMID 14696386 DOI: 10.1016/S0076-6879(03)74021-X  0.624
2003 Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 53: 430-5. PMID 14579332 DOI: 10.1002/Prot.10550  0.72
2000 Petrey D, Honig B. Free energy determinants of tertiary structure and the evaluation of protein models Protein Science. 9: 2181-2191. PMID 11152128 DOI: 10.1110/Ps.9.11.2181  0.627
1999 Norel R, Petrey D, Wolfson HJ, Nussinov R. Examination of shape complementarity in docking of unbound proteins. Proteins. 36: 307-17. PMID 10409824 DOI: 10.1002/(Sici)1097-0134(19990815)36:3<307::Aid-Prot5>3.0.Co;2-R  0.456
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