(Q30360455)

11 November 2017

Near-native structure refinement using in vacuo energy minimization. (English)

1 reference

11 November 2017

2

Michael Levitt

1 reference

11 November 2017

Christopher M Summa

1

1 reference

PMC publication ID

1802011

11 November 2017

language of work or name

English

0 references

publication date

20 February 2007

1 reference

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

11 November 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

11 November 2017

104

1 reference

11 November 2017

9

1 reference

11 November 2017

3177-3182

1 reference

Physically realistic homology models built with ROSETTA can be more accurate than their templates

11 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

GROMACS: fast, flexible, and free

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Progress over the first decade of CASP experiments.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

An atomic environment potential for use in protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

The limit of accuracy of protein modeling: influence of crystal packing on protein 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=1802011

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

A quantum mechanical polarizable force field for biomolecular interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Exploring the helix-coil transition via all-atom equilibrium ensemble 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=1802011

Making optimal use of empirical energy functions: force-field parameterization in crystal space

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Homology-based modelling of targets for rational drug 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=1802011

The state of the Protein Structure Initiative.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

The ASTRAL Compendium in 2004

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing 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=1802011

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

The ASTRAL compendium for protein structure and sequence analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Packing of sidechains in low-resolution models for 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=1802011

Influence of protein structure databases on the predictive power of statistical pair potentials

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

CATH--a hierarchic classification of protein domain structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

SCOP: a structural classification of proteins database for the investigation of sequences and structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Energy refinement of hen egg-white lysozyme

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Computation of structures of homologous proteins. .alpha.-Lactalbumin from lysozyme

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802011

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular 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=1802011

Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function.

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

Statistical potentials extracted from protein structures: how accurate are they?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

On the limited memory BFGS method for large scale optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0611593104

Structural biology. Structural genomics, round 2

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17360625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Refinement of protein conformations using a macromolecular energy minimization procedure

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17360625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0611593104

1 reference

11 November 2017

0 references

1 reference

PMC publication ID

1802011

11 November 2017

PubMed publication ID

17360625

1 reference

PMC publication ID

1802011