Molecular dynamics simulation for all
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …
has expanded dramatically in recent years. These simulations capture the behavior of …
Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and
studies of functional materials. Over the past decade, various coherent nonlinear vibrational …
studies of functional materials. Over the past decade, various coherent nonlinear vibrational …
gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS
MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …
most popular methods to estimate binding free energies. This method has been proven to …
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape,–, have activity
against diverse sarbecoviruses,,–, and be highly protective through viral neutralization,,–and …
against diverse sarbecoviruses,,–, and be highly protective through viral neutralization,,–and …
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
AmberTools
AmberTools | Journal of Chemical Information and Modeling ACS ACS Publications C&EN CAS
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved variants with
substitutions in the spike receptor-binding domain (RBD) that affect its affinity for angiotensin …
substitutions in the spike receptor-binding domain (RBD) that affect its affinity for angiotensin …
Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study
J Wang - Journal of chemical information and modeling, 2020 - ACS Publications
The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
MDTraj: a modern open library for the analysis of molecular dynamics trajectories
As molecular dynamics (MD) simulations continue to evolve into powerful computational
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …
[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
world to perform in silico simulations and modelings on diverse scientific topics, especially in …