(Q38985037)

8 September 2017

title

Effective protein model structure refinement by loop modeling and overall relaxation (English)

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8 September 2017

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3

Chaok Seok

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8 September 2017

1

Gyu Rie Lee

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8 September 2017

2

Lim Heo

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8 September 2017

language of work or name

English

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publication date

14 July 2015

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8 September 2017

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8 September 2017

volume

84 Suppl 1

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8 September 2017

page(s)

293-301

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Protein structure prediction: when is it useful?

8 September 2017

cites work

1 reference

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Homology modeling in drug discovery: current trends and applications

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Evaluating the usefulness of protein structure models for molecular replacement.

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Protein structure prediction and structural genomics

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Progress and challenges in protein structure prediction

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Molecular dynamics in the endgame of protein structure prediction.

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Can molecular dynamics simulations provide high-resolution refinement of protein structure?

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Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.

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Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

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Solvent dramatically affects protein structure refinement.

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Refinement of homology-based protein structures by molecular dynamics simulation techniques

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Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

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

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Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering

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Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

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Specific interactions for ab initio folding of protein terminal regions with secondary structures.

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Near-native structure refinement using in vacuo energy minimization.

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

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

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Protein model refinement using an optimized physics-based all-atom force field

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Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling

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Evaluation of predictions in the CASP10 model refinement category.

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Improved prediction of protein side-chain conformations with SCWRL4

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Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

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Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

21 January 2018

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Protein loop modeling by using fragment assembly and analytical loop closure

21 January 2018

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A kinematic view of loop closure

21 January 2018

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Assessment of CASP7 predictions for template-based modeling targets

21 January 2018

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CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

21 January 2018

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MolProbity: all-atom structure validation for macromolecular crystallography

21 January 2018

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Refinement of protein termini in template-based modeling using conformational space annealing

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21 January 2018

Identifiers

DOI

10.1002/PROT.24858

1 reference

8 September 2017

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