(Q49265475)

19 February 2018

title

Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. (English)

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19 February 2018

author name string

Tappura K

series ordinal

1

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19 February 2018

language of work or name

English

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publication date

1 August 2001

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19 February 2018

published in

Proteins

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19 February 2018

volume

44

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19 February 2018

issue

3

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19 February 2018

page(s)

167-179

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19 February 2018

Optimization by Simulated Annealing

cites work

1 reference

Modeling of protein loops by simulated annealing

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A structure refinement method based on molecular dynamics in four spatial dimensions.

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Global energy minimization by rotational energy embedding.

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An approach to the multiple-minima problem by relaxing dimensionality

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Conformational search by potential energy annealing: algorithm and application to cyclosporin A.

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Local elevation: a method for improving the searching properties of molecular dynamics simulation.

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Protein folding by restrained energy minimization and molecular dynamics

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Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. Circumventing problems associated with folding

21 January 2018

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van der Waals Volumes and Radii

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Progress in protein structure prediction

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Conformations of immunoglobulin hypervariable regions

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PDB-based protein loop prediction: parameters for selection and methods for optimization.

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Reversible peptide folding in solution by molecular dynamics simulation.

21 January 2018

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Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings

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Evaluation of the conformational free energies of loops in proteins.

21 January 2018

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Does conformational free energy distinguish loop conformations in proteins?

21 January 2018

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Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions

21 January 2018

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WHAT IF: a molecular modeling and drug design program

21 January 2018

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Errors in protein structures

21 January 2018

1 reference

Folding proteins with a simple energy function and extensive conformational searching

21 January 2018

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

Structure Optimization Combining Soft-Core Interaction Functions, the Diffusion Equation Method, and Molecular Dynamics

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Loop closure via bond scaling and relaxation

21 January 2018

1 reference

Three-dimensional structure of the apo form of the N-terminal EGF-like module of blood coagulation factor X as determined by NMR spectroscopy and simulated folding

21 January 2018

1 reference

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

21 January 2018

1 reference

Prediction of loop geometries using a generalized born model of solvation effects

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/PROT.1082

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19 February 2018

PubMed ID

11455590

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19 February 2018