In silico methods and tools for drug discovery
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …
develop new drugs, but the process from lead identification to clinical trials takes more than …
Molecular docking and structure-based drug design strategies
Pharmaceutical research has successfully incorporated a wealth of molecular modeling
methods, within a variety of drug discovery programs, to study complex biological and …
methods, within a variety of drug discovery programs, to study complex biological and …
Modeling and simulations of polymers: a roadmap
TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …
engineering community. These computational approaches enable predictions and provide …
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Motivation: Molecular simulation has historically been a low-throughput technique, but faster
computers and increasing amounts of genomic and structural data are changing this by …
computers and increasing amounts of genomic and structural data are changing this by …
Phosphorus-enhanced and calcium-retarded transport of ferrihydrite colloid: mechanism of electrostatic potential changes regulated via adsorption speciation
J Ma, J Li, L Weng, X Ouyang, Y Chen… - Environmental Science & …, 2023 - ACS Publications
The transport of ferrihydrite colloid (FHC) through porous media is influenced by anions (eg,
PO43–) and cations (eg, Ca2+) in the aqueous environment. This study investigated the …
PO43–) and cations (eg, Ca2+) in the aqueous environment. This study investigated the …
An automated force field topology builder (ATB) and repository: version 1.0
The Automated force field Topology Builder (ATB, http://compbio. biosci. uq. edu. au/atb) is a
Web-accessible server that can provide topologies and parameters for a wide range of …
Web-accessible server that can provide topologies and parameters for a wide range of …
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
N Schmid, AP Eichenberger, A Choutko… - European biophysics …, 2011 - Springer
New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are
introduced. These parameter sets summarise some previously published force field …
introduced. These parameter sets summarise some previously published force field …
Molecular dynamics simulations and drug discovery
JD Durrant, JA McCammon - BMC biology, 2011 - Springer
This review discusses the many roles atomistic computer simulations of macromolecular (for
example, protein) receptors and their associated small-molecule ligands can play in drug …
example, protein) receptors and their associated small-molecule ligands can play in drug …
CHARMM‐GUI: a web‐based graphical user interface for CHARMM
CHARMM is an academic research program used widely for macromolecular mechanics
and dynamics with versatile analysis and manipulation tools of atomic coordinates and …
and dynamics with versatile analysis and manipulation tools of atomic coordinates and …
GROMACS: fast, flexible, and free
This article describes the software suite GROMACS (Groningen MAchine for Chemical
Simulation) that was developed at the University of Groningen, The Netherlands, in the early …
Simulation) that was developed at the University of Groningen, The Netherlands, in the early …