(Q30369502)

13 October 2017

pmx: Automated protein structure and topology generation for alchemical perturbations. (English)

1 reference

13 October 2017

1 reference

1

Vytautas Gapsys

1 reference

13 October 2017

Servaas Michielssens

2

1 reference

13 October 2017

Daniel Seeliger

series ordinal

3

1 reference

13 October 2017

Bert L de Groot

series ordinal

4

1 reference

13 October 2017

8 December 2014

1 reference

Journal of Computational Chemistry

13 October 2017

1 reference

13 October 2017

36

1 reference

13 October 2017

5

1 reference

13 October 2017

348-354

1 reference

A designed conformational shift to control protein binding specificity.

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Towards computational specificity screening of DNA-binding proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Recent advances in computational protein design.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

How robust are protein folding simulations with respect to force field parameterization?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Protein thermostability calculations using alchemical free energy simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Improved side-chain torsion potentials for the Amber ff99SB protein force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Performance of protein stability predictors.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Macromolecular modeling with rosetta

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

A three-state prediction of single point mutations on protein stability changes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Canonical sampling through velocity rescaling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Comparison of multiple Amber force fields and development of improved protein backbone parameters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

A simple physical model for binding energy hot spots in protein-protein complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Computational design of protein-protein interactions.

3 June 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

21 January 2018

1 reference

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

21 January 2018

1 reference

Prediction of protein conformational freedom from distance constraints

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4365728

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25487359

12 December 2020

inferred from PubMed ID database lookup

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25487359

12 December 2020

inferred from PubMed ID database lookup

Predicting free energy changes using structural ensembles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25487359

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/JCC.23804

1 reference

13 October 2017

journals/jcc/GapsysMSG15

1 reference

DBLP Dataset 2021-01-02

release_kqoxu2dxb5b53f25sgry3rq7ga

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kqoxu2dxb5b53f25sgry3rq7ga

24 November 2022

mapped directly with Wikidata item

1 reference

13 October 2017

PubMed publication ID

25487359

1 reference