(Q42182344)

18 October 2017

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes (English)

1 reference

principal component analysis

18 October 2017

0 references

0 references

4

Robert L Jernigan

1 reference

18 October 2017

3

Alicia Carriquiry

1 reference

18 October 2017

Lei Yang

1

1 reference

PMCID

2350220

18 October 2017

Guang Song

series ordinal

2

1 reference

18 October 2017

1 February 2008

1 reference

18 October 2017

1 reference

18 October 2017

16

1 reference

18 October 2017

321-330

1 reference

18 October 2017

2

1 reference

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

vGNM: a better model for understanding the dynamics of proteins in crystals

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

The role of shape in determining molecular motions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

An analysis of core deformations in protein superfamilies

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Mining frequent patterns in protein structures: a study of protease families.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

How to describe protein motion without amino acid sequence and atomic coordinates.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Principal components analysis of protein structure ensembles calculated using NMR data.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Anisotropy of fluctuation dynamics of proteins with an elastic network model

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

26 October 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Essential dynamics of proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Dynamics of folded proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Conformational change of proteins arising from normal mode calculations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

An efficient method for sampling the essential subspace of proteins.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Functional motions can be extracted from on‐lattice construction of protein structures

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

A motion planning approach to flexible ligand binding.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2350220

Analysis of domain motions in large proteins

1 December 2018

1 reference

12 December 2020

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

1 reference

12 December 2020

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

1 reference

12 December 2020

Understanding protein flexibility through dimensionality reduction

1 reference

12 December 2020

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

12 December 2020

10.1016/J.STR.2007.12.011

Identifiers

DOI

1 reference

18 October 2017

1 reference

18 October 2017

1 reference

PMCID

2350220