(Q35887173)

10 August 2017

Locating binding poses in protein-ligand systems using reconnaissance metadynamics (English)

1 reference

10 August 2017

3

Michele Parrinello

1 reference

10 August 2017

Pär Söderhjelm

1

1 reference

PMCID

3325676

10 August 2017

Gareth A Tribello

series ordinal

2

1 reference

PMCID

3325676

10 August 2017

language of work or name

English

0 references

publication date

21 March 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

10 August 2017

1 reference

10 August 2017

109

1 reference

10 August 2017

14

1 reference

10 August 2017

5170-5175

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Pathway and mechanism of drug binding to G-protein-coupled receptors.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

SwissDock, a protein-small molecule docking web service based on EADock DSS

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

How does a drug molecule find its target binding site?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Advances in all atom sampling methods for modeling protein-ligand binding affinities

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Advances and challenges in protein-ligand docking

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

A self-learning algorithm for biased molecular dynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Systematic determination of order parameters for chain dynamics using diffusion maps.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

λ-Dynamics free energy simulation methods

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Canonical sampling through velocity rescaling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Calculation of protein-ligand binding affinities.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

A critical assessment of docking programs and scoring functions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Calculation of absolute protein-ligand binding free energy from computer simulations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Flexible docking in solution using metadynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Escaping free-energy minima

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Efficient docking of peptides to proteins without prior knowledge of the binding site

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Energetics of glycerol conduction through aquaglyceroporin GlpF.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Developing a dynamic pharmacophore model for HIV-1 integrase.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

An automated method for dynamic ligand design.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Tyrosine 151 is part of the substrate activation binding site of bovine trypsin. Identification by covalent labeling with p-diazoniumbenzamidine and kinetic characterization of Tyr-151-(p-benzamidino)-azo-beta-trypsin

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Fast docking using the CHARMM force field with EADock DSS.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: a survivin example.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Inclusion mechanism of steroid drugs into beta-cyclodextrins. Insights from free energy calculations.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Exploring complex protein-ligand recognition mechanisms with coarse metadynamics

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Blind docking of 260 protein-ligand complexes with EADock 2.0.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Receptor rigidity and ligand mobility in trypsin-ligand complexes

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

Assessing scoring functions for protein-ligand interactions

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325676

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1201940109

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1201940109

Enhanced Configurational Sampling in Binding Free-Energy Calculations

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1201940109

A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22440749

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22440749

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1201940109

1 reference

10 August 2017

0 references

1 reference

10 August 2017

1 reference

PMCID

3325676