Structure-guided forcefield optimization (Q41927287)

14 October 2017

Structure-guided forcefield optimization (English)

1 reference

14 October 2017

David Baker

5

0 references

Andrew Leaver-Fay

series ordinal

3

object named as

Andrew Leaver-Fay

1 reference

14 October 2017

Yifan Song

1

1 reference

14 October 2017

Michael Tyka

series ordinal

2

1 reference

14 October 2017

James Thompson

series ordinal

4

1 reference

14 October 2017

language of work or name

English

0 references

publication date

12 April 2011

1 reference

14 October 2017

1 reference

14 October 2017

79

1 reference

14 October 2017

6

1 reference

14 October 2017

1898-1909

1 reference

Alternate states of proteins revealed by detailed energy landscape mapping

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Atomic-Level Characterization of the Structural Dynamics of Proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Structure prediction for CASP8 with all-atom refinement using Rosetta.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Improved prediction of protein side-chain conformations with SCWRL4

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Progress in modeling of protein structures and interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

PISCES: recent improvements to a PDB sequence culling server

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

The HHpred interactive server for protein homology detection and structure prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Modeling structurally variable regions in homologous proteins with rosetta.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Protein structure prediction using Rosetta

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

PISCES: a protein sequence culling server

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Rotamer libraries in the 21st century

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Twist and shear in beta-sheets and beta-ribbons.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Development and current status of the CHARMM force field for nucleic acids.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Comparison of database potentials and molecular mechanics force fields

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

An iterative method for extracting energy-like quantities from protein structures.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Structure-derived potentials and protein simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Hydrogen bonding in globular proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Critical assessment of methods of protein structure prediction - Round VIII.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Protein-protein docking with backbone flexibility

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

The contribution of C alpha-H...O hydrogen bonds to membrane protein stability depends on the position of the amide

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Improved treatment of the protein backbone in empirical force fields.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Coulombic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in pr

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3457920

An all atom force field for simulations of proteins and nucleic acids

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002/PROT.23013

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002/PROT.23013

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21488100

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.23013

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.23013

A new force field for molecular mechanical simulation of nucleic acids and proteins

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.23013

Identifiers

DOI

10.1002/PROT.23013

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

21488100

1 reference