(Q30409188)

8 November 2017

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics (English)

1 reference

molecular dynamics simulation

8 November 2017

0 references

1 reference

2

1 reference

8 November 2017

4

Michael R Shirts

1 reference

8 November 2017

Kai Wang

1

1 reference

PMC publication ID

4154199

8 November 2017

Yanzhi Yang

series ordinal

3

1 reference

8 November 2017

3 December 2013

1 reference

Journal of Computer - Aided Molecular Design

8 November 2017

1 reference

8 November 2017

27

1 reference

8 November 2017

12

1 reference

8 November 2017

989-1007

1 reference

https://scigraph.springernature.com/pub.10.1007/s10822-013-9689-8

8 November 2017

0 references

cites work

Exchange Often and Properly in Replica Exchange Molecular Dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

OpenMM: A Hardware Independent Framework for Molecular Simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

How does a drug molecule find its target binding site?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Alchemical free energy methods for drug discovery: progress and challenges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Atomic-level characterization of the structural dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Virtual screening: an endless staircase?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Identifying and characterizing binding sites and assessing druggability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Accelerating molecular dynamic simulation on graphics processing units

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Managing protein flexibility in docking and its applications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Computations of standard binding free energies with molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Investigation of MM-PBSA rescoring of docking poses

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Predicting absolute ligand binding free energies to a simple model site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

A critical assessment of docking programs and scoring functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Automatic atom type and bond type perception in molecular mechanical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

The Amber biomolecular simulation programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Soft docking and multiple receptor conformations in virtual screening

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Development and testing of a general amber force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Testing a flexible-receptor docking algorithm in a model binding site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

A model binding site for testing scoring functions in molecular docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

SuperStar: improved knowledge-based interaction fields for protein binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Automated docking of substrates to proteins by simulated annealing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4154199

Molecular docking with ligand attached water molecules.

20 June 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Evaluation of different virtual screening programs for docking in a charged binding pocket

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Anton, a special-purpose machine for molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Let's get honest about sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Protein-ligand binding free energies from exhaustive docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

A solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Density-Based Clustering in Spatial Databases: The Algorithm GDBSCAN and Its Applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Two-dimensional replica-exchange method for predicting protein-ligand binding structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-013-9689-8

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24297454

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-013-9689-8

1 reference

8 November 2017

journals/jcamd/WangCYS13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4154199

8 November 2017

PubMed publication ID

24297454

1 reference

PMC publication ID

4154199