Funnel metadynamics as accurate binding free-energy method (Q30539051)

16 August 2017

Funnel metadynamics as accurate binding free-energy method (English)

1 reference

16 August 2017

Vittorio Limongelli

1

0 references

Michele Parrinello

series ordinal

3

object named as

Michele Parrinello

1 reference

16 August 2017

Massimiliano Bonomi

2

1 reference

PMCID

3631651

16 August 2017

language of work or name

English

0 references

publication date

3 April 2013

1 reference

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

16 August 2017

1 reference

16 August 2017

110

1 reference

16 August 2017

6358-6363

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16 August 2017

16

1 reference

Standard binding free energies from computer simulations: What is the best strategy?

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Sampling protein motion and solvent effect during ligand binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Complete reconstruction of an enzyme-inhibitor binding process by 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=3631651

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=3631651

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

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=3631651

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Calculation 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=3631651

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Calculation of absolute protein-ligand binding free energy from computer 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=3631651

Flexible docking in solution using metadynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

The many roles of computation in drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Energetics of ion conduction through the gramicidin channel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Escaping free-energy minima

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active 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=3631651

The statistical-thermodynamic basis for computation of binding affinities: a critical review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Expression and selective inhibition of the constitutive and inducible forms of human cyclo-oxygenase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

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=3631651

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3631651

Automated docking with grid-based energy evaluation

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1303186110

Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method

21 January 2018

1 reference

12 December 2020

A new method for predicting binding affinity in computer-aided drug design

1 reference

12 December 2020

Thermodynamic analysis of binding of p-substituted benzamidines to trypsin

1 reference

12 December 2020

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

1 reference

12 December 2020

Uncovering molecular details of urea crystal growth in the presence of additives

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1303186110

1 reference

16 August 2017

0 references

1 reference

16 August 2017

1 reference

PMCID

3631651