Search Results - "Durrant, Jacob D"

BlendMol: advanced macromolecular visualization in Blender by Durrant, Jacob D

“…Programs such as VMD and PyMOL are excellent tools for analyzing macromolecular structures, but they do not implement many of the advanced rendering techniques…”
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Molecular dynamics simulations and drug discovery by Durrant, Jacob D, McCammon, J Andrew

“…This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule…”
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NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function by Durrant, Jacob D, McCammon, J. Andrew

“…NNScore is a neural-network-based scoring function designed to aid the computational identification of small-molecule ligands. While the test cases included in…”
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POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics by Durrant, Jacob D, Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E

“…Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in…”
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AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization by Spiegel, Jacob O., Durrant, Jacob D.

“…We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted…”
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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs by Wagner, Jeffrey R, Lee, Christopher T, Durrant, Jacob D, Malmstrom, Robert D, Feher, Victoria A, Amaro, Rommie E

“…Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date,…”
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Teaching old docks new tricks with machine learning enhanced ensemble docking by Bhatt, Roshni, Wang, Ann, Durrant, Jacob D.

“…We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble…”
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Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery by Wang, Ann, Durrant, Jacob D

“…We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in…”
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MolModa: accessible and secure molecular docking in a web browser by Kochnev, Yuri, Ahmed, Mayar, Maldonado, Alex M, Durrant, Jacob D

“…Molecular docking advances early-stage drug discovery by predicting the geometries and affinities of small-molecule compounds bound to drug-target receptors,…”
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NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes by Durrant, Jacob D, McCammon, J. Andrew

“…As high-throughput biochemical screens are both expensive and labor intensive, researchers in academia and industry are turning increasingly to…”
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ProteinVR: Web-based molecular visualization in virtual reality by Cassidy, Kevin C, Šefčík, Jan, Raghav, Yogindra, Chang, Alexander, Durrant, Jacob D

“…Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education…”
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From byte to bench to bedside: molecular dynamics simulations and drug discovery by Ahmed, Mayar, Maldonado, Alex M, Durrant, Jacob D

“…Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer…”
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Computational approaches to mapping allosteric pathways by Feher, Victoria A, Durrant, Jacob D, Van Wart, Adam T, Amaro, Rommie E

“…•Advances in computational methods for allosteric pathways are reviewed.•New methods are able to replicate many but not all experimental results.•Each method…”
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FPocketWeb: protein pocket hunting in a web browser by Kochnev, Yuri, Durrant, Jacob D.

“…Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection…”
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Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics by Hellemann, Erich, Walker, Jennifer L, Lesko, Mitchell A, Chandrashekarappa, Dakshayini G, Schmidt, Martin C, O'Donnell, Allyson F, Durrant, Jacob D

“…Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases…”
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Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants by Durrant, Jacob D, Bush, Robin M, Amaro, Rommie E

“…Deletions in the stalk of the influenza neuraminidase (NA) surface protein are associated with increased virulence, but the mechanisms responsible for this…”
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Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism by Durrant, Jacob D, Kochanek, Sarah E, Casalino, Lorenzo, Ieong, Pek U, Dommer, Abigail C, Amaro, Rommie E

“…Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and occasional pandemic outbreaks. Influenza neuraminidase, a viral…”
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Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae by Lesko, Mitchell A, Chandrashekarappa, Dakshayini G, Jordahl, Eric M, Oppenheimer, Katherine G, Bowman, 2nd, Ray W, Shang, Chaowei, Durrant, Jacob D, Schmidt, Martin C, O'Donnell, Allyson F

“…Glucose is the preferred carbon source for most eukaryotes, and the first step in its metabolism is phosphorylation to glucose-6-phosphate. This reaction is…”
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LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry by Durrant, Jacob D, Amaro, Rommie E

“…As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes…”
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Capturing the Mechanism Underlying TOP mRNA Binding to LARP1 by Cassidy, Kevin C., Lahr, Roni M., Kaminsky, Jesse C., Mack, Stephanie, Fonseca, Bruno D., Das, Subha R., Berman, Andrea J., Durrant, Jacob D.

“…The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine…”
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