Recovering physical potentials from a model protein databank (Q34358926)

1 August 2017

Recovering physical potentials from a model protein databank (English)

1 reference

1 August 2017

J W Mullinax

1

1 reference

PubMed ID

21041685

1 August 2017

W G Noid

series ordinal

2

1 reference

PubMed ID

21041685

1 August 2017

language of work or name

English

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publication date

1 November 2010

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

1 August 2017

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1 August 2017

107

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1 August 2017

46

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1 August 2017

19867-19872

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Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Performance of the Pro-sp3-TASSER server in CASP8

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Generic coarse-grained model for protein folding and aggregation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

OPUS-Rota: a fast and accurate method for side-chain modeling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Binding-induced folding of a natively unstructured transcription factor.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Potential energy functions for protein design.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Statistical potential for assessment and prediction of protein structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Knowledge-based potentials in protein design.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Relation between native ensembles and experimental structures of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

A composite score for predicting errors in protein structure models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

A new generation of statistical potentials for proteins.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

In quest of an empirical potential for protein structure prediction.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

GROMACS: fast, flexible, and free

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Coarse-grained normal mode analysis in structural biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Coarse-grained models for proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

The dependence of all-atom statistical potentials on structural training database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Development of novel statistical potentials for protein fold recognition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Announcing the worldwide Protein Data Bank

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Boltzmann-type distribution of side-chain conformation in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Coarse-grained sequences for protein folding and design

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Molecular dynamics simulations of biomolecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Matching simulation and experiment: a new simplified model for simulating protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Effective energy functions for protein structure prediction.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Knowledge-based potentials--back to the roots

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

How do potentials derived from structural databases relate to "true" potentials?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Comparison of database potentials and molecular mechanics force fields

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

How to derive a protein folding potential? A new approach to an old problem

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

From Levinthal to pathways to funnels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Protein function in the crystal

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Structure-derived potentials and protein simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

How optimization of potential functions affects protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

An empirical energy function for threading protein sequence through the folding motif

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Reduced representation model of protein structure prediction: statistical potential and genetic algorithms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Knowledge-based potentials for proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

A computer model to dynamically simulate protein folding: studies with crambin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Metastability of the folded states of globular proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

The nature of folded states of globular proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Optimal protein-folding codes from spin-glass theory

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Protein folding funnels: a kinetic approach to the sequence-structure relationship

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Contact potential that recognizes the correct folding of globular proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Computer simulation of protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993375

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Generalized Yvon-Born-Green theory for molecular systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Multiscale coarse graining of liquid-state systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Maximum Entropy Approach for Deducing Amino Acid Interactions in Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1006428107

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

21 January 2018

1 reference

12 December 2020

The histidyl residues in ribonuclease-S. Photooxidation in solution and in single crystals; the iodination of histidine-12

1 reference

12 December 2020

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

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12 December 2020

Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein

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12 December 2020

Extracting contact energies from protein structures: a study using a simplified model

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12 December 2020

A multiscale coarse-graining method for biomolecular systems

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12 December 2020

Another look at the conditions for the extraction of protein knowledge-based potentials

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12 December 2020

Identifiers

DOI

10.1073/PNAS.1006428107

1 reference

1 August 2017

0 references

1 reference

1 August 2017

1 reference

PubMed ID

21041685