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Biochemical simulations

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Jacob Beal, Ting Lu, Ron Weiss

Molecular docking, simulation and binding free energy analysis of small molecules as PfHT1 inhibitors

Afolabi J. Owoloye, Funmilayo C. Ligali, [ ... ], Kolapo M. Oyebola

Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology

Kun-Yi Hsin, Samik Ghosh, Hiroaki Kitano

Computational Predictions of Volatile Anesthetic Interactions with the Microtubule Cytoskeleton: Implications for Side Effects of General Anesthesia

Travis J. A. Craddock, Marc St. George, [ ... ], Jack A. Tuszynski

A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli

Akintunde Emiola, John George, Steven S. Andrews

Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

Aruna Rajan, Peter L. Freddolino, Klaus Schulten

In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation

M. Iqbal Choudhary, Muniza Shaikh, Atia- tul-Wahab, Atta- ur-Rahman

Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan-PPAR Partial Agonists

Marcelo Vizoná Liberato, Alessandro S. Nascimento, [ ... ], Igor Polikarpov

Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Ji-Long Zhang, Qing-Chuan Zheng, Zheng-Qiang Li, Hong-Xing Zhang

Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies

Nagasundaram N, Hailong Zhu, [ ... ], Luonan Chen

Homology Modeling of Dopamine D₂ and D₃ Receptors: Molecular Dynamics Refinement and Docking Evaluation

Chiara Bianca Maria Platania, Salvatore Salomone, [ ... ], Claudio Bucolo

Modeling Symmetric Macromolecular Structures in Rosetta3

Frank DiMaio, Andrew Leaver-Fay, [ ... ], Ingemar André

Modeling the Time Evolution of the Nanoparticle-Protein Corona in a Body Fluid

Daniele Dell'Orco, Martin Lundqvist, [ ... ], Sara Linse

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