(Q30403868)

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Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21674234%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models (English)

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4 February 2020

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Michael T. Zimmermann

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4 February 2020

Robert L Jernigan

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object named as

Robert L Jernigan

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4 February 2020

Andrzej Kloczkowski

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Andrzej Kloczkowski

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4 February 2020

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Sumudu P Leelananda

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4 February 2020

Pawel Gniewek

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4 February 2020

Yaping Feng

4

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4 February 2020

publication date

15 June 2011

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4 February 2020

Journal of Structural and Functional Genomics

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4 February 2020

12

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4 February 2020

2

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4 February 2020

137-147

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4 February 2020

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases

1 reference

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20 June 2018

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Computer-aided design of functional protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Backbone flexibility in computational protein design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

A guide to template based structure prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Quality assessment of protein structure models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Convergence and combination of methods in protein-protein docking

1 reference

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20 June 2018

FINDSITE: a combined evolution/structure-based approach to protein function prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Enzyme (re)design: lessons from natural evolution and computation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Computational methods for calculation of ligand-binding affinity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Protein structure prediction and model quality assessment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Contrasting disease and nondisease protein aggregation by molecular simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Conformational stability and folding mechanisms of dimeric proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Predicting 3D structures of protein-protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Recent Progress and Future Directions in Protein-Protein Docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Packing regularities in biological structures relate to their dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Coarse-grained normal mode analysis in structural biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Inferring ideal amino acid interaction forms from statistical protein contact potentials

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Protein decoy sets for evaluating energy functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

A normalized root-mean-square distance for comparing protein three-dimensional structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Anisotropy of fluctuation dynamics of proteins with an elastic network model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

A database of macromolecular motions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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1 reference

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

20 June 2018

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1 reference

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1 reference

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1 reference

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20 June 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227679

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Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

1 reference

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The Protein Data Bank: a computer-based archival file for macromolecular structures

1 reference

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20 June 2018

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

1 reference

https://api.crossref.org/works/10.1007%2FS10969-011-9113-3

21 January 2018

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

1 reference

https://api.crossref.org/works/10.1007%2FS10969-011-9113-3

21 January 2018

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1 reference

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1 reference

https://api.crossref.org/works/10.1007%2FS10969-011-9113-3

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Geometric cooperativity and anticooperativity of three-body interactions in native proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/21674234

12 December 2020

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10.1007/S10969-011-9113-3

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4 February 2020

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4 February 2020

PubMed publication ID

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Europe PubMed Central

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4 February 2020

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