Structure-derived potentials and protein simulations (Q41052933)

26 September 2017

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title

Structure-derived potentials and protein simulations (English)

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26 September 2017

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Jernigan RL

1

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PubMed ID

8728652

26 September 2017

Bahar I

series ordinal

2

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26 September 2017

1 April 1996

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Current Opinion in Structural Biology

26 September 2017

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26 September 2017

6

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26 September 2017

2

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26 September 2017

195-209

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A simplified representation of protein conformations for rapid simulation of protein folding

26 September 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Assessment of protein models with three-dimensional profiles

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A new approach to protein fold recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Protein structure prediction based on statistical potential

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

An improved pair potential to recognize native protein folds

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Predicting coiled coils by use of pairwise residue correlations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

An analysis of incorrectly folded protein models. Implications for structure predictions.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Criteria that discriminate between native proteins and incorrectly folded models

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Discriminating compact nonnative structures from the native structure of globular proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Proteins with selected sequences fold into unique native conformation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Theoretical studies of protein folding and unfolding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Enlarged representative set of protein structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Conformations of folded proteins in restricted spaces

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A new substitution matrix for protein sequence searches based on contact frequencies in protein structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Protein stability for single substitution mutants and the extent of local compactness in the denatured state

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Ranking potential binding peptides to MHC molecules by a computational threading approach

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Hydrophobic potential by pairwise surface area sum.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Knowledge-based potentials for proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Contact potential that recognizes the correct folding of globular proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A new protein folding recognition potential function

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Progress in fold recognition.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

From structure to sequence and back again.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Optimal sequence selection in proteins of known structure by simulated evolution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Computer simulation of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Funnels, pathways, and the energy landscape of protein folding: a synthesis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Exploring conformational space with a simple lattice model for protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A simplified amino acid potential for use in structure predictions of proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Principles of protein folding--a perspective from simple exact models.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Side-chain entropy and packing in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

How does a protein fold?

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Forces of tertiary structural organization in globular proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

The complexity and accuracy of discrete state models of protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Prediction of the folding pathways and structure of the GCN4 leucine zipper

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A new computational model for protein folding based on atomic solvation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Folding protein alpha-carbon chains into compact forms by Monte Carlo methods

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Lattice model simulations of polypeptide chain folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

LINUS: a hierarchic procedure to predict the fold of a protein.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A model of myoglobin self-organization

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Pseudodihedrals: simplified protein backbone representation with knowledge-based energy

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Pseudotorsional OCCO backbone angle as a single descriptor of protein secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Context is a major determinant of β-sheet propensity

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Consistencies of individual DNA base-amino acid interactions in structures and sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

Recognizing native folds by the arrangement of hydrophobic and polar residues

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980075-3

7 January 2021

10.1016/S0959-440X(96)80075-3

Identifiers

DOI

1 reference

26 September 2017

1 reference

PubMed ID

8728652