Jacob D. Durrant

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 17

Top Topics

Molecular Dynamics Simulations

Virtual Screening

Top Venues

J. Cheminformatics

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Roshni Bhatt, David Ryan Koes, Jacob D. Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. J. Chem. Inf. Model. 64 (12) (2024)
Jade Young, Neerja Garikipati, Jacob D. Durrant
BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript. J. Chem. Inf. Model. 62 (4) (2022)
Jacob D. Durrant
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization. J. Comput. Aided Mol. Des. 36 (9) (2022)
Yuri Kochnev, Jacob D. Durrant
FPocketWeb: protein pocket hunting in a web browser. J. Cheminformatics 14 (1) (2022)
Erich Hellemann, Jennifer L. Walker, Mitchell A. Lesko, Dakshayini G. Chandrashekarappa, Martin C. Schmidt, Allyson F. O'Donnell, Jacob D. Durrant
Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PLoS Comput. Biol. 18 (3) (2022)
Harrison Green, Jacob D. Durrant
DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization. J. Chem. Inf. Model. 61 (6) (2021)
Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinform. 36 (16) (2020)
Kevin C. Cassidy, Jan Sefcik, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
ProteinVR: Web-based molecular visualization in virtual reality. PLoS Comput. Biol. 16 (3) (2020)
Emily J. Ha, Cara T. Lwin, Jacob D. Durrant
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. J. Cheminformatics 12 (1) (2020)
Jacob O. Spiegel, Jacob D. Durrant
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J. Cheminformatics 12 (1) (2020)
Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe, Jacob D. Durrant
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J. Cheminformatics 11 (1) (2019)
Jacob D. Durrant
BlendMol: advanced macromolecular visualization in Blender. Bioinform. 35 (13) (2019)
Patrick J. Ropp, Jesse C. Kaminsky, Sara Yablonski, Jacob D. Durrant
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. J. Cheminformatics 11 (1) (2019)
Sayuri Pacheco, Jesse C. Kaminsky, Iurii K. Kochnev, Jacob D. Durrant
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. J. Chem. Inf. Model. 59 (10) (2019)
Nivedita Rajendiran, Jacob D. Durrant
Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques. J. Comput. Chem. 39 (12) (2018)
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
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. J. Cheminformatics 10 (1) (2018)
Patrick J. Ropp, Aaron J. Friedman, Jacob D. Durrant
Scoria: a Python module for manipulating 3D molecular data. J. Cheminformatics 9 (1) (2017)
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
A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. J. Chem. Inf. Model. 55 (2) (2015)
Jacob D. Durrant, Kathryn E. Carlson, Teresa A. Martin, Tavina L. Offutt, Christopher G. Mayne, John A. Katzenellenbogen, Rommie E. Amaro
Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J. Chem. Inf. Model. 55 (9) (2015)
Jacob D. Durrant, Rommie E. Amaro
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinform. 15 (2014)
Jacob D. Durrant, Rommie E. Amaro
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. PLoS Comput. Biol. 10 (7) (2014)
Jacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon
Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. J. Chem. Inf. Model. 53 (7) (2013)
Jacob D. Durrant, James Andrew McCammon
. PLoS Comput. Biol. 8 (3) (2012)
Jacob D. Durrant, James Andrew McCammon
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inf. Model. 51 (11) (2011)
Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon
CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Inf. Model. 51 (10) (2011)
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
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6 (1) (2010)
Jacob D. Durrant, James Andrew McCammon
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Inf. Model. 50 (10) (2010)
Jacob D. Durrant, James Andrew McCammon
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput. Biol. Chem. 34 (2) (2010)