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Author Details

Jacob D Durrant
University of Pittsburgh
2006
71
28
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36906819Allosteric inhibition of TEM-1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights.Protein Sci2023
37251500Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv2023
37196001Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae.PLoS Genet2023
35235554Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics.PLoS Comput Biol2022
35843309Phosphate position is key in mediating transmembrane ion channel TMEM16A-phosphatidylinositol 4,5-bisphosphate interaction.J Biol Chem2022
35889494Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery.Molecules2022
36008829FPocketWeb: protein pocket hunting in a web browser.J Cheminform2022
36008698Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization.J Comput Aided Mol Des2022
35129332BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript.J Chem Inf Model2022
35149760Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance.Commun Biol2022
34194693DeepFrag: a deep convolutional neural network for fragment-based lead optimization.Chem Sci2021
33940558PARP1: Structural insights and pharmacological targets for inhibition.DNA Repair (Amst)2021
34029094DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization.J Chem Inf Model2021
32559277Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser.Bioinformatics2020
33431021AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization.J Cheminform2020
33292486LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates.J Cheminform2020
32605926MutantHuntWGS: A Pipeline for Identifying <i>Saccharomyces cerevisiae</i> Mutations.G3 (Bethesda)2020
32123736Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism.ACS Cent Sci2020
32231351ProteinVR: Web-based molecular visualization in virtual reality.PLoS Comput Biol2020
30481283BlendMol: advanced macromolecular visualization in Blender.Bioinformatics2019
31676287Capturing the Mechanism Underlying TOP mRNA Binding to LARP1.Structure2019
31584859Characterization of Female Reproductive Proteases in a Butterfly from Functional and Evolutionary Perspectives.Physiol Biochem Zool2019
31580061PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser.J Chem Inf Model2019
31127411Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.J Cheminform2019
30767086Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.J Cheminform2019
29280166Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.J Comput Chem2018
30555910A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target.ACS Cent Sci2018
29464421Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies.J Cheminform2018
27977118Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast.ACS Chem Biol2017
28453915Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs.Chem Biol Drug Des2017
29086076Scoria: a Python module for manipulating 3D molecular data.J Cheminform2017
27074285Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.Chem Rev2016
27141956Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants.J Phys Chem B2016
27291296Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor.Sci Rep2016
25521642Machine-learning techniques applied to antibacterial drug discovery.Chem Biol Drug Des2015
26286148Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.J Chem Inf Model2015
25555059A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity.J Chem Inf Model2015
24667124Computational approaches to mapping allosteric pathways.Curr Opin Struct Biol2014
25284249Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase.Bioorg Med Chem2014
25400521POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.J Chem Theory Comput2014
25032790LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.PLoS Comput Biol2014
24803851Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis.J Chem Theory Comput2014
24886360WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.BMC Bioinformatics2014
23734946Comparing neural-network scoring functions and the state of the art: applications to common library screening.J Chem Inf Model2013
23792207AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.J Mol Graph Model2013
22613098Novel cruzain inhibitors for the treatment of Chagas' disease.Chem Biol Drug Des2012
22438795AutoClickChem: click chemistry in silico.PLoS Comput Biol2012
22487100The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness.Chem Biol Drug Des2012
22594624LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders.Chem Biol Drug Des2012
21147010POVME: an algorithm for measuring binding-pocket volumes.J Mol Graph Model2011
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Collaborators

James Andrew McCammon
Co-authored papers 26
Rommie E Amaro
University of California
Co-authored papers 18
Gregory M Goldgof
University of California san francisco
Co-authored papers 4
Edgar Vigil
University of California
Co-authored papers 4
Sabine Ottilie
University of California San Diego
Co-authored papers 4
Jennifer Yang
Chang Gung Memorial Hospital
Co-authored papers 3
Elizabeth A Winzeler
University of California San Diego
Co-authored papers 3
Jake Schenken
University of California
Co-authored papers 3
Felicia Gunawan
University of California
Co-authored papers 3
Robert V Swift
University of California San Diego
Co-authored papers 2
Victoria A Feher
University of California San Diego
Co-authored papers 2
Andrea L Cheung
University of California
Co-authored papers 2
Case W McNamara
a division of The Scripps Research Institute La Jolla
Co-authored papers 2
Prianka Kumar
The George Washington University School of Medicine and Health Sciences
Co-authored papers 2
Allyson F O'Donnell
University of Pittsburgh
Co-authored papers 2
Luke Whitesell
University of Toronto
Co-authored papers 1
Alasdair C Steven
National Institutes of Health
Co-authored papers 1
Reysha Patel
University of California
Co-authored papers 1
Allison K Doak
Department of Pharmaceutical Chemistry, University of California San Francisco
Co-authored papers 1
William H Gerwick
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 1
Bennett Van Houten
UPMC-Hillman Cancer Center, University of Pittsburgh
Co-authored papers 1
Matthew Abraham
University of California
Co-authored papers 1
Emmanuelle LeBlanc
University of Toronto
Co-authored papers 1
Amanda K Lukens
Harvard T.H. Chan School of Public Health
Co-authored papers 1
Yoshiyuki Suzuki
Nagoya City University
Co-authored papers 1
Dyann F Wirth
The Broad Institute
Co-authored papers 1
Gisel Lopez
University of California
Co-authored papers 1
Karla P Godinez-Macias
University of California
Co-authored papers 1
Madeline R Luth
University of California San Diego
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Roy M Williams
University of California
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Release 1.2