Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines

Labute, M X; Zhang, X; Lenderman, J; Bennion, B; Wong, S E; Lightstone, F C

doi:10.1371/journal.pone.0106298

Title: Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines

Journal Article · Fri Mar 07 00:00:00 EST 2014 · PLOS ONE, N/A, N/A, September 5, 2014, N/A

DOI:https://doi.org/10.1371/journal.pone.0106298· OSTI ID:1169266

Labute, M X; Zhang, X; Lenderman, J; Bennion, B; Wong, S E; Lightstone, F C

View Journal Article

Cite

Export

Save

Research Organization:: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: DE-AC52-07NA27344

OSTI ID:: 1169266

Report Number(s):: LLNL-JRNL-652054

Journal Information:: PLOS ONE, N/A, N/A, September 5, 2014, N/A, Journal Name: PLOS ONE, N/A, N/A, September 5, 2014, N/A

Country of Publication:: United States

Language:: English

References (73)

The Gene Ontology (GO) database and informatics resource Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh036	journal	January 2004
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A _2A Receptor Lenselink, Eelke B.; Beuming, Thijs; Sherman, Woody Journal of Chemical Information and Modeling, Vol. 54, Issue 6 https://doi.org/10.1021/ci5000455	journal	May 2014
Analysis of drug-induced effect patterns to link structure and side effects of medicines Fliri, Anton F.; Loging, William T.; Thadeio, Peter F. Nature Chemical Biology, Vol. 1, Issue 7 https://doi.org/10.1038/nchembio747	journal	November 2005
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level: Metal-Binding Site Prediction by FINDSITE-Metal Brylinski, Michal; Skolnick, Jeffrey Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 3 https://doi.org/10.1002/prot.22913	journal	December 2010
The Economic Costs of Diabetes: Is It Time for a New Treatment Paradigm? Herman, W. H. Diabetes Care, Vol. 36, Issue 4 https://doi.org/10.2337/dc13-0270	journal	March 2013
Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces Yamanishi, Yoshihiro; Pauwels, Edouard; Kotera, Masaaki Journal of Chemical Information and Modeling, Vol. 52, Issue 12 https://doi.org/10.1021/ci2005548	journal	December 2012
Benchmarking Sets for Molecular Docking Huang, Niu; Shoichet, Brian K.; Irwin, John J. Journal of Medicinal Chemistry, Vol. 49, Issue 23 https://doi.org/10.1021/jm0608356	journal	November 2006
Investigation of MM-PBSA Rescoring of Docking Poses Thompson, David C.; Humblet, Christine; Joseph-McCarthy, Diane Journal of Chemical Information and Modeling, Vol. 48, Issue 5 https://doi.org/10.1021/ci700470c	journal	April 2008
Generalized Born Model with a Simple, Robust Molecular Volume Correction Mongan, John; Simmerling, Carlos; McCammon, J. Andrew Journal of Chemical Theory and Computation, Vol. 3, Issue 1 https://doi.org/10.1021/ct600085e	journal	December 2006
Genome-wide association analysis by lasso penalized logistic regression Wu, Tong Tong; Chen, Yi Fang; Hastie, Trevor Bioinformatics, Vol. 25, Issue 6 https://doi.org/10.1093/bioinformatics/btp041	journal	January 2009
Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment Zhang, Xiaohua; Wong, Sergio E.; Lightstone, Felice C. Journal of Chemical Information and Modeling, Vol. 54, Issue 1 https://doi.org/10.1021/ci4005145	journal	December 2013
Protein-ligand docking: Current status and future challenges Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 1 https://doi.org/10.1002/prot.21082	journal	July 2006
Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures Huang, Liang-Chin; Wu, Xiaogang; Chen, Jake Y. PROTEOMICS, Vol. 13, Issue 2 https://doi.org/10.1002/pmic.201200337	journal	January 2013
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors Xie, Li; Li, Jerry; Xie, Lei PLoS Computational Biology, Vol. 5, Issue 5 https://doi.org/10.1371/journal.pcbi.1000387	journal	May 2009
Analysis of acute-phase proteins, AHSG, C3, CLI, HP and SAA, reveals distinctive expression patterns associated with breast, colorectal and lung cancer Dowling, Paul; Clarke, Colin; Hennessy, Kim International Journal of Cancer, Vol. 131, Issue 4 https://doi.org/10.1002/ijc.26462	journal	November 2011
Predicting drug side-effects by chemical systems biology Tatonetti, Nicholas P.; Liu, Tianyun; Altman, Russ B. Genome Biology, Vol. 10, Issue 9 https://doi.org/10.1186/gb-2009-10-9-238	journal	January 2009
Large-scale prediction and testing of drug activity on side-effect targets Lounkine, Eugen; Keiser, Michael J.; Whitebread, Steven Nature, Vol. 486, Issue 7403 https://doi.org/10.1038/nature11159	journal	June 2012
Exploring protein native states and large-scale conformational changes with a modified generalized born model Onufriev, Alexey; Bashford, Donald; Case, David A. Proteins: Structure, Function, and Bioinformatics, Vol. 55, Issue 2 https://doi.org/10.1002/prot.20033	journal	March 2004
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking Mysinger, Michael M.; Carchia, Michael; Irwin, John. J. Journal of Medicinal Chemistry, Vol. 55, Issue 14 https://doi.org/10.1021/jm300687e	journal	July 2012
Profilin acts downstream of LDL to mediate diabetic endothelial cell dysfunction Romeo, Giulio; V. Frangioni, John; Kazlauskas, Andrius The FASEB Journal, Vol. 18, Issue 6 https://doi.org/10.1096/fj.03-0841fje	journal	February 2004
A side effect resource to capture phenotypic effects of drugs Kuhn, Michael; Campillos, Monica; Letunic, Ivica Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2009.98	journal	January 2010
Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C. Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt403	journal	May 2013
Accounting for water molecules in drug design Wong, Sergio E.; Lightstone, Felice C. Expert Opinion on Drug Discovery, Vol. 6, Issue 1 https://doi.org/10.1517/17460441.2011.534452	journal	November 2010
Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field Sousa, S. F.; Ribeiro, A. J. M.; Coimbra, J. T. S. Current Medicinal Chemistry, Vol. 20, Issue 18 https://doi.org/10.2174/0929867311320180002	journal	April 2013
Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis Scheiber, Josef; Chen, Bin; Milik, Mariusz Journal of Chemical Information and Modeling, Vol. 49, Issue 2 https://doi.org/10.1021/ci800344p	journal	January 2009
Altered expression of apoptotic factors and synaptic markers in postmortem brain from bipolar disorder patients Kim, Hyung-Wook; Rapoport, Stanley I.; Rao, Jagadeesh S. Neurobiology of Disease, Vol. 37, Issue 3 https://doi.org/10.1016/j.nbd.2009.11.010	journal	March 2010
A Critical Assessment of Docking Programs and Scoring Functions Warren, Gregory L.; Andrews, C. Webster; Capelli, Anna-Maria Journal of Medicinal Chemistry, Vol. 49, Issue 20 https://doi.org/10.1021/jm050362n	journal	October 2006
Evaluation of docking programs for predicting binding of Golgi α-mannosidase II inhibitors: A comparison with crystallography Englebienne, Pablo; Fiaux, Hélène; Kuntz, Douglas A. Proteins: Structure, Function, and Bioinformatics, Vol. 69, Issue 1 https://doi.org/10.1002/prot.21479	journal	June 2007
Thromboxane A ₂ receptor-mediated release of matrix metalloproteinase-1 (MMP-1) induces expression of monocyte chemoattractant protein-1 (MCP-1) by activation of protease-activated receptor 2 (PAR2) in A549 human lung adenocarcinoma cells: PAR2 MEDIATES MMP-1-INDUCED MCP-1 EXPRESSION Li, Xiuling; Tai, Hsin-Hsiung Molecular Carcinogenesis, Vol. 53, Issue 8 https://doi.org/10.1002/mc.22020	journal	March 2013
Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design Zhang, Xiaohua; Gibbs, Alan C.; Reynolds, Charles H. Journal of Chemical Information and Modeling, Vol. 50, Issue 4 https://doi.org/10.1021/ci9003333	journal	March 2010
Drug-Related Morbidity and Mortality: Updating the Cost-of-Illness Model Ernst, Frank R.; Grizzle, Amy J. Journal of the American Pharmaceutical Association (1996), Vol. 41, Issue 2 https://doi.org/10.1016/S1086-5802(16)31229-3	journal	March 2001
Cell Distribution Differences Of Matrix Metalloproteinase-9 and Tissue Inhibitor of Matrix Metalloproteinase-1 in Patients With Kawasaki Disease Korematsu, Seigo; Ohta, Yoko; Tamai, Naotaka The Pediatric Infectious Disease Journal, Vol. 31, Issue 9 https://doi.org/10.1097/INF.0b013e31825ba6b3	journal	January 2012
Role of the Protein Tyrosine Kinase Syk in Regulating Cell-Cell Adhesion and Motility in Breast Cancer Cells Zhang, X.; Shrikhande, U.; Alicie, B. M. Molecular Cancer Research, Vol. 7, Issue 5 https://doi.org/10.1158/1541-7786.MCR-08-0371	journal	May 2009
SuperTarget and Matador: resources for exploring drug-target relationships Gunther, S.; Kuhn, M.; Dunkel, M. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm862	journal	December 2007
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines Zhang, Xiaohua; Wong, Sergio E.; Lightstone, Felice C. Journal of Computational Chemistry, Vol. 34, Issue 11 https://doi.org/10.1002/jcc.23214	journal	January 2013
Heart failure events with rosiglitazone in type 2 diabetes: data from the RECORD clinical trial Komajda, M.; McMurray, J. J. V.; Beck-Nielsen, H. European Heart Journal, Vol. 31, Issue 7 https://doi.org/10.1093/eurheartj/ehp604	journal	January 2010
Drug Target Identification Using Side-Effect Similarity Campillos, M.; Kuhn, M.; Gavin, A. -C. Science, Vol. 321, Issue 5886 https://doi.org/10.1126/science.1158140	journal	July 2008
Areas, Volumes, Packing, and Protein Structure Richards, F. M. Annual Review of Biophysics and Bioengineering, Vol. 6, Issue 1 https://doi.org/10.1146/annurev.bb.06.060177.001055	journal	June 1977
Predicting Adverse Drug Events Using Pharmacological Network Models Cami, A.; Arnold, A.; Manzi, S. Science Translational Medicine, Vol. 3, Issue 114 https://doi.org/10.1126/scitranslmed.3002774	journal	December 2011
Identifying and Characterizing Binding Sites and Assessing Druggability Halgren, Thomas A. Journal of Chemical Information and Modeling, Vol. 49, Issue 2 https://doi.org/10.1021/ci800324m	journal	January 2009
MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization Guimarães, Cristiano R. W.; Cardozo, Mario Journal of Chemical Information and Modeling, Vol. 48, Issue 5 https://doi.org/10.1021/ci800004w	journal	April 2008
Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap Yang, Yue; Lightstone, Felice C.; Wong, Sergio E. Expert Opinion on Drug Discovery, Vol. 8, Issue 3 https://doi.org/10.1517/17460441.2013.749853	journal	January 2013
The effect of hyperthyroidism on procoagulant, anticoagulant and fibrinolytic factors: A systematic review and meta-analysis Stuijver, Danka; Zaane, Bregje van; Romualdi, Erica Thrombosis and Haemostasis, Vol. 108, Issue 12 https://doi.org/10.1160/TH12-07-0496	journal	January 2012
Increased susceptibility to apoptosis in cultured fibroblasts from antipsychotic-naïve first-episode schizophrenia patients Gassó, Patricia; Mas, Sergi; Molina, Oriol Journal of Psychiatric Research, Vol. 48, Issue 1 https://doi.org/10.1016/j.jpsychires.2013.09.017	journal	January 2014
Syk Tyrosine Kinase Acts as a Pancreatic Adenocarcinoma Tumor Suppressor by Regulating Cellular Growth and Invasion Layton, Tracy; Stalens, Cristel; Gunderson, Felizza The American Journal of Pathology, Vol. 175, Issue 6 https://doi.org/10.2353/ajpath.2009.090543	journal	December 2009
Beta2-integrin activation on T cell subsets is an independent prognostic factor in unstable angina pectoris Konstandin, Mathias H.; Aksoy, Hülya; Wabnitz, Guido H. Basic Research in Cardiology, Vol. 104, Issue 3 https://doi.org/10.1007/s00395-008-0770-8	journal	January 2009
Reducing safety-related drug attrition: the use of in vitro pharmacological profiling Bowes, Joanne; Brown, Andrew J.; Hamon, Jacques Nature Reviews Drug Discovery, Vol. 11, Issue 12 https://doi.org/10.1038/nrd3845	journal	November 2012
The Medical Dictionary for Regulatory Activities (MedDRA) Brown, Elliot G.; Wood, Louise; Wood, Sue Drug Safety, Vol. 20, Issue 2 https://doi.org/10.2165/00002018-199920020-00002	journal	January 1999
Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure Nilmeier, Jerome P.; Kirshner, Daniel A.; Wong, Sergio E. PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0062535	journal	May 2013
Predicting adverse side effects of drugs Huang, Liang-Chin; Wu, Xiaogang; Chen, Jake Y. BMC Genomics, Vol. 12, Issue Suppl 5 https://doi.org/10.1186/1471-2164-12-S5-S11	journal	January 2011
Relating drug-protein interaction network with drug side effects Mizutani, S.; Pauwels, E.; Stoven, V. Bioinformatics, Vol. 28, Issue 18 https://doi.org/10.1093/bioinformatics/bts383	journal	September 2012
Systematic identification of proteins that elicit drug side effects Kuhn, Michael; Al Banchaabouchi, Mumna; Campillos, Monica Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2013.10	journal	January 2013
Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization Cobanoglu, Murat Can; Liu, Chang; Hu, Feizhuo Journal of Chemical Information and Modeling, Vol. 53, Issue 12 https://doi.org/10.1021/ci400219z	journal	December 2013
Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome Yang, Lun; Chen, Jian; He, Lin PLoS Computational Biology, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pcbi.1000441	journal	July 2009
MMP1, MMP9, and COX2 Expressions in Promonocytes Are Induced by Breast Cancer Cells and Correlate with Collagen Degradation, Transformation-Like Morphological Changes in MCF-10A Acini, and Tumor Aggressiveness Chimal-Ramírez, G. K.; Espinoza-Sánchez, N. A.; Utrera-Barillas, D. BioMed Research International, Vol. 2013 https://doi.org/10.1155/2013/279505	journal	January 2013
Chemical space Kirkpatrick, Peter; Ellis, Clare Nature, Vol. 432, Issue 7019 https://doi.org/10.1038/432823a	journal	December 2004
A geometric approach to macromolecule-ligand interactions Kuntz, Irwin D.; Blaney, Jeffrey M.; Oatley, Stuart J. Journal of Molecular Biology, Vol. 161, Issue 2 https://doi.org/10.1016/0022-2836(82)90153-X	journal	October 1982
Cardiovascular events associated with rofecoxib: final analysis of the APPROVe trial Baron, John A.; Sandler, Robert S.; Bresalier, Robert S. The Lancet, Vol. 372, Issue 9651 https://doi.org/10.1016/S0140-6736(08)61490-7	journal	November 2008
High-energy water sites determine peptide binding affinity and specificity of PDZ domains Beuming, Thijs; Farid, Ramy; Sherman, Woody Protein Science, Vol. 18, Issue 8 https://doi.org/10.1002/pro.177	journal	August 2009
A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways Wallach, Izhar; Jaitly, Navdeep; Lilien, Ryan PLoS ONE, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pone.0012063	journal	August 2010
Comparative Evaluation of 11 Scoring Functions for Molecular Docking Wang, Renxiao; Lu, Yipin; Wang, Shaomeng Journal of Medicinal Chemistry, Vol. 46, Issue 12 https://doi.org/10.1021/jm0203783	journal	June 2003
Regularization Paths for Generalized Linear Models via Coordinate Descent Friedman, Jerome; Hastie, Trevor; Tibshirani, Robert Journal of Statistical Software, Vol. 33, Issue 1 https://doi.org/10.18637/jss.v033.i01	journal	January 2010
Inhibitor Ranking through QM Based Chelation Calculations for Virtual Screening of HIV-1 RNase H Inhibition Poongavanam, Vasanthanathan; Steinmann, Casper; Kongsted, Jacob PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0098659	journal	June 2014
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Predicting drug side-effect profiles: a chemical fragment-based approach Pauwels, Edouard; Stoven, Véronique; Yamanishi, Yoshihiro BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-169	journal	January 2011
When good drugs go bad Giacomini, Kathleen M.; Krauss, Ronald M.; Roden, Dan M. Nature, Vol. 446, Issue 7139 https://doi.org/10.1038/446975a	journal	April 2007
Statistical significance for genomewide studies Storey, J. D.; Tibshirani, R. Proceedings of the National Academy of Sciences, Vol. 100, Issue 16, p. 9440-9445 https://doi.org/10.1073/pnas.1530509100	journal	July 2003
The role of quantum mechanics in structure-based drug design Raha, Kaushik; Peters, Martin B.; Wang, Bing Drug Discovery Today, Vol. 12, Issue 17-18 https://doi.org/10.1016/j.drudis.2007.07.006	journal	September 2007
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go: Docking/scoring methods-a review Moitessier, N.; Englebienne, P.; Lee, D. British Journal of Pharmacology, Vol. 153, Issue S1 https://doi.org/10.1038/sj.bjp.0707515	journal	March 2008
Project ranks billions of drug interactions Reardon, Sara Nature, Vol. 503, Issue 7477 https://doi.org/10.1038/503449a	journal	November 2013
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs Liu, Mei; Wu, Yonghui; Chen, Yukun Journal of the American Medical Informatics Association, Vol. 19, Issue e1 https://doi.org/10.1136/amiajnl-2011-000699	journal	June 2012
Keynote review: In vitro safety pharmacology profiling: an essential tool for successful drug development Whitebread, Steven; Hamon, Jacques; Bojanic, Dejan Drug Discovery Today, Vol. 10, Issue 21 https://doi.org/10.1016/S1359-6446(05)03632-9	journal	November 2005

Similar Records

Message Passing Interface and Multithreading Hybrid for Parallel Molecular Docking of Large Databases on Petascale High Performance Computing Machines

Journal Article · Mon Jul 30 00:00:00 EDT 2012 · Journal of Computational Chemistry · OSTI ID:1169266

Zhang, X; Wong, S E; Lightstone, F C

Towards fully automated high performance computing drug discovery: A massively parallel virtual screening pipeline for docking and MM/GBSA rescoring to improve enrichment

Journal Article · Fri Aug 23 00:00:00 EDT 2013 · Journal of Chemical Information and Modeling, na, na, December 20, 2013, pp. 324-337 · OSTI ID:1169266

Zhang, X; Wong, S E; Lightstone, F C

Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction

Journal Article · Thu Oct 28 00:00:00 EDT 2021 · Journal of Computer-Aided Molecular Design · OSTI ID:1169266

Demerdash, Omar A.

Related Subjects

97 MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
59 BASIC BIOLOGICAL SCIENCES

Title: Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines

Citation Formats

References (73)

Similar Records

Related Subjects