Jacob D. Durrant

28 papers Journal 28
YearRankTypeTitle / Venue / Authors
2024 J jnl
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks.
J. Chem. Inf. Model.
Roshni Bhatt, David Ryan Koes, Jacob D. Durrant
2022 J jnl
BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript.
J. Chem. Inf. Model.
Jade Young, Neerja Garikipati, Jacob D. Durrant
2022 J jnl
FPocketWeb: protein pocket hunting in a web browser.
J. Cheminformatics
Yuri Kochnev, Jacob D. Durrant
2022 J jnl
Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics.
PLoS Comput. Biol.
Erich Hellemann, Jennifer L. Walker, Mitchell A. Lesko, Dakshayini G. Chandrashekarappa, Martin C. Schmidt, Allyson F. O'Donnell, Jacob D. Durrant
2022 J jnl
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization.
J. Comput. Aided Mol. Des.
Jacob D. Durrant
2021 J jnl
DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization.
J. Chem. Inf. Model.
Harrison Green, Jacob D. Durrant
2020 J jnl
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization.
J. Cheminformatics
Jacob O. Spiegel, Jacob D. Durrant
2020 J jnl
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates.
J. Cheminformatics
Emily J. Ha, Cara T. Lwin, Jacob D. Durrant
2020 J jnl
ProteinVR: Web-based molecular visualization in virtual reality.
PLoS Comput. Biol.
Kevin C. Cassidy, Jan Sefcik, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
2020 J jnl
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser.
Bioinform.
Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty
2019 J jnl
BlendMol: advanced macromolecular visualization in Blender.
Bioinform.
Jacob D. Durrant
2019 J jnl
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.
J. Cheminformatics
Patrick J. Ropp, Jesse C. Kaminsky, Sara Yablonski, Jacob D. Durrant
2019 J jnl
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.
J. Cheminformatics
Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe, Jacob D. Durrant
2019 J jnl
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser.
J. Chem. Inf. Model.
Sayuri Pacheco, Jesse C. Kaminsky, Iurii K. Kochnev, Jacob D. Durrant
2018 J jnl
Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.
J. Comput. Chem.
Nivedita Rajendiran, Jacob D. Durrant
2018 J jnl
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies.
J. Cheminformatics
Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki, Jacob D. Durrant
2017 J jnl
Scoria: a Python module for manipulating 3D molecular data.
J. Cheminformatics
Patrick J. Ropp, Aaron J. Friedman, Jacob D. Durrant
2015 J jnl
A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity.
J. Chem. Inf. Model.
Nur Kusaira Khairul Ikram, Jacob D. Durrant, Muchtaridi Muchtaridi, Ayunni Salihah Zalaludin, Neny Purwitasari, Nornisah Mohamed, Aisyah Saad Abdul Rahim, Chan Kit Lam, Yahaya M. Normi, Noorsaadah Abdul Rahman, Rommie E. Amaro, Habibah A. Wahab
2015 J jnl
Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.
J. Chem. Inf. Model.
Jacob D. Durrant, Kathryn E. Carlson, Teresa A. Martin, Tavina L. Offutt, Christopher G. Mayne, John A. Katzenellenbogen, Rommie E. Amaro
2014 J jnl
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry.
PLoS Comput. Biol.
Jacob D. Durrant, Rommie E. Amaro
2014 J jnl
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.
BMC Bioinform.
Jacob D. Durrant, Rommie E. Amaro
2013 J jnl
Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening.
J. Chem. Inf. Model.
Jacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon
2012 J jnl
AutoClickChem: Click Chemistry
PLoS Comput. Biol.
Jacob D. Durrant, James Andrew McCammon
2011 J jnl
CrystalDock: A Novel Approach to Fragment-Based Drug Design.
J. Chem. Inf. Model.
Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon
2011 J jnl
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function.
J. Chem. Inf. Model.
Jacob D. Durrant, James Andrew McCammon
2010 J jnl
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
PLoS Comput. Biol.
Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon
2010 J jnl
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes.
J. Chem. Inf. Model.
Jacob D. Durrant, James Andrew McCammon
2010 J jnl
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design.
Comput. Biol. Chem.
Jacob D. Durrant, James Andrew McCammon