Publications by authors named "Jacob D Durrant"

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Teaching old docks new tricks with machine learning enhanced ensemble docking.
Roshni Bhatt, Ann Wang, Jacob D Durrant

Sci Rep· September 2024

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MolModa: accessible and secure molecular docking in a web browser.
Yuri Kochnev, Mayar Ahmed, Alex M Maldonado, Jacob D Durrant

Nucleic Acids Res· July 2024

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The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during infection.
Charles Agbavor, Adriana Zimnicka, Allison Kumar, Jada L George, Madeline Torres, Jacob D Durrant

mBio· July 2024

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CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks.
Roshni Bhatt, David Ryan Koes, Jacob D Durrant

J Chem Inf Model· June 2024

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Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution.
Nick Barts, Roshni H Bhatt, Chelsea Toner, Wynn K Meyer, Jacob D Durrant

Comp Biochem Physiol B Biochem Mol Biol· February 2024

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From byte to bench to bedside: molecular dynamics simulations and drug discovery.
Mayar Ahmed, Alex M Maldonado, Jacob D Durrant

BMC Biol· December 2023

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Genome mining yields putative disease-associated ROMK variants with distinct defects.
Nga H Nguyen, Srikant Sarangi, Erin M McChesney, Shaohu Sheng, Jacob D Durrant

PLoS Genet· November 2023

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From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery.
Mayar Ahmed, Alex M Maldonado, Jacob D Durrant

ArXiv· November 2023

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CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks.
Roshni Bhatt, David Ryan Koes, Jacob D Durrant

bioRxiv· October 2023

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Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.
Erich Hellemann, Jacob D Durrant

J Chem Theory Comput· September 2023

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Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics.
Arie van Wieren, Jacob D Durrant, Sudipta Majumdar

Drug Dev Res· August 2023

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Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae.
Mitchell A Lesko, Dakshayini G Chandrashekarappa, Eric M Jordahl, Katherine G Oppenheimer, Ray W Bowman, Jacob D Durrant

PLoS Genet· May 2023

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Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.
Erich Hellemann, Jacob D Durrant

bioRxiv· May 2023

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Allosteric inhibition of TEM-1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights.
Erich Hellemann, Amrita Nallathambi, Jacob D Durrant

Protein Sci· April 2023

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Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization.
Jacob D Durrant

J Comput Aided Mol Des· September 2022

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Phosphate position is key in mediating transmembrane ion channel TMEM16A-phosphatidylinositol 4,5-bisphosphate interaction.
Maiwase Tembo, Rachel E Bainbridge, Crystal Lara-Santos, Kayla M Komondor, Grant J Daskivich, Jacob D Durrant

J Biol Chem· August 2022

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FPocketWeb: protein pocket hunting in a web browser.
Yuri Kochnev, Jacob D Durrant

J Cheminform· August 2022

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Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery.
Ann Wang, Jacob D Durrant

Molecules· July 2022

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Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics.
Erich Hellemann, Jennifer L Walker, Mitchell A Lesko, Dakshayini G Chandrashekarappa, Martin C Schmidt, Jacob D Durrant

PLoS Comput Biol· March 2022

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BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript.
Jade Young, Neerja Garikipati, Jacob D Durrant

J Chem Inf Model· February 2022

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Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance.
Sabine Ottilie, Madeline R Luth, Erich Hellemann, Gregory M Goldgof, Eddy Vigil, Jacob D Durrant

Commun Biol· February 2022

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PARP1: Structural insights and pharmacological targets for inhibition.
Jacob O Spiegel, Bennett Van Houten, Jacob D Durrant

DNA Repair (Amst)· July 2021

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DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization.
Harrison Green, Jacob D Durrant

J Chem Inf Model· June 2021

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DeepFrag: a deep convolutional neural network for fragment-based lead optimization.
Harrison Green, David R Koes, Jacob D Durrant

Chem Sci· May 2021

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AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization.
Jacob O Spiegel, Jacob D Durrant

J Cheminform· April 2020

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