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Xiaohua Zhang, Ph.D. - Publications

Affiliations: 
2007 Chemistry University of California, Santa Barbara, Santa Barbara, CA, United States 
Area:
bioorganic and bioinorganic chemistry
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21 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 Stevenson GA, Kirshner D, Bennion BJ, Yang Y, Zhang X, Zemla A, Torres MW, Epstein A, Jones D, Kim H, Bennett WFD, Wong SE, Allen JE, Lightstone FC. Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. Journal of Chemical Information and Modeling. PMID 37847557 DOI: 10.1021/acs.jcim.3c00722  0.562
2023 Fan YJ, Allen JE, McLoughlin KS, Shi D, Bennion BJ, Zhang X, Lightstone FC. Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction. Artificial Intelligence Chemistry. 1. PMID 37583465 DOI: 10.1016/j.aichem.2023.100004  0.553
2023 Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, et al. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure. Journal of Chemical Theory and Computation. PMID 37075065 DOI: 10.1021/acs.jctc.2c01018  0.57
2022 López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, et al. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. Journal of Chemical Theory and Computation. PMID 35866871 DOI: 10.1021/acs.jctc.2c00168  0.575
2022 Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, et al. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophysical Journal. PMID 35778842 DOI: 10.1016/j.bpj.2022.06.035  0.536
2022 Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, et al. Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 34983849 DOI: 10.1073/pnas.2113297119  0.549
2021 Lau EY, Negrete OA, Bennett WFD, Bennion BJ, Borucki M, Bourguet F, Epstein A, Franco M, Harmon B, He S, Jones D, Kim H, Kirshner D, Lao V, Lo J, ... ... Zhang X, et al. Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. Frontiers in Molecular Biosciences. 8: 678701. PMID 34327214 DOI: 10.3389/fmolb.2021.678701  0.538
2021 Jones D, Kim H, Zhang X, Zemla A, Stevenson G, Bennett WFD, Kirshner D, Wong SE, Lightstone FC, Allen JE. Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. Journal of Chemical Information and Modeling. PMID 33754707 DOI: 10.1021/acs.jcim.0c01306  0.59
2020 Zhang X, Sundram S, Oppelstrup T, Kokkila-Schumacher SIL, Carpenter TS, Ingólfsson HI, Streitz FH, Lightstone FC, Glosli JN. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. The Journal of Chemical Physics. 153: 045103. PMID 32752727 DOI: 10.1063/5.0014500  0.537
2020 Zhu F, Zhang X, Allen J, Jones D, Lightstone FC. Binding Affinity Prediction by Pairwise Function Based on Neural Network. Journal of Chemical Information and Modeling. PMID 32338892 DOI: 10.1021/acs.jcim.0c00026  0.573
2018 Cranford JP, O'Hara TJ, Villongco CT, Hafez OM, Blake RC, Loscalzo J, Fattebert JL, Richards DF, Zhang X, Glosli JN, McCulloch AD, Krummen DE, Lightstone FC, Wong SE. Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study. Cardiovascular Engineering and Technology. PMID 29549620 DOI: 10.1007/S13239-018-0347-0  0.54
2016 Zhang X, Perez-Sanchez H, Lightstone FC. A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin. Current Topics in Medicinal Chemistry. PMID 27852201  0.56
2014 LaBute MX, Zhang X, Lenderman J, Bennion BJ, Wong SE, Lightstone FC. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. Plos One. 9: e106298. PMID 25191698 DOI: 10.1371/Journal.Pone.0106298  0.553
2014 Zhang X, Wong SE, Lightstone FC. 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. Journal of Chemical Information and Modeling. 54: 324-37. PMID 24358939 DOI: 10.1021/ci4005145  0.58
2013 Zhang X, Wong SE, Lightstone FC. Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines. Journal of Computational Chemistry. 34: 915-27. PMID 23345155 DOI: 10.1002/jcc.23214  0.548
2008 Zhang X, Bruice TC. Complexation of single strand telomere and telomerase RNA template polyanions by deoxyribonucleic guanidine (DNG) polycations: plausible anticancer agents. Bioorganic & Medicinal Chemistry Letters. 18: 665-9. PMID 18063368 DOI: 10.1016/J.Bmcl.2007.11.061  0.435
2007 Zhang X, Bruice TC. Diels-Alder ribozyme catalysis: a computational approach. Journal of the American Chemical Society. 129: 1001-7. PMID 17243837 DOI: 10.1021/Ja067416I  0.368
2007 Zhang X, Bruice TC. Temperature-dependent structure of the E x S complex of Bacillus stearothermophilus alcohol dehydrogenase. Biochemistry. 46: 837-43. PMID 17223705 DOI: 10.1021/Bi062110+  0.424
2006 Zhang X, Bruice TC. Temperature dependence of the structure of the substrate and active site of the Thermus thermophilus chorismate mutase E x S complex. Biochemistry. 45: 8562-7. PMID 16834330 DOI: 10.1021/Bi0604227  0.451
2005 Zhang X, Bruice TC. The proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction. Proceedings of the National Academy of Sciences of the United States of America. 102: 18356-60. PMID 16344484 DOI: 10.1073/Pnas.0509234102  0.467
2005 Zhang X, Zhang X, Bruice TC. A definitive mechanism for chorismate mutase. Biochemistry. 44: 10443-8. PMID 16060652 DOI: 10.1021/Bi050886P  0.449
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