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Biochemical simulations

A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing

Nithishwer Mouroug Anand, Devang Haresh Liya, [ ... ], Ashwin Kumar Jainarayanan

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin

Systematic Validation of Protein Force Fields against Experimental Data

Kresten Lindorff-Larsen, Paul Maragakis, [ ... ], David E. Shaw

Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations

Sunhwan Jo, Taehoon Kim, Wonpil Im

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Jenna L. Morgan, Aaron E. Darling, Jonathan A. Eisen

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast

Maria I. Davidich, Stefan Bornholdt

The Molecular Mechanism of Bisphenol A (BPA) as an Endocrine Disruptor by Interacting with Nuclear Receptors: Insights from Molecular Dynamics (MD) Simulations

Lanlan Li, Qianqian Wang, [ ... ], Huanxiang Liu

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

Kota Kasahara, Ikuo Fukuda, Haruki Nakamura

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

Ramy K. Aziz, Scott Devoid, [ ... ], Fangfang Xia

Inhibitory Effect of mTOR Activator MHY1485 on Autophagy: Suppression of Lysosomal Fusion

Yeon Ja Choi, Yun Jung Park, [ ... ], Hae Young Chung

BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

Thomas E. Gorochowski, Antoni Matyjaszkiewicz, [ ... ], Mario di Bernardo

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

Jacob Beal, Ting Lu, Ron Weiss

Detailed Enzyme Kinetics in Terms of Biochemical Species: Study of Citrate Synthase

Daniel A. Beard, Kalyan C. Vinnakota, Fan Wu

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