RASP: rapid modeling of protein side chain conformations (Q30407480)

21 June 2017

RASP: rapid modeling of protein side chain conformations (English)

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21 June 2017

Zhichao Miao

1

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21 June 2017

Yang Cao

series ordinal

2

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21 June 2017

Taijiao Jiang

series ordinal

3

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21 June 2017

language of work or name

English

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publication date

23 September 2011

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21 June 2017

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21 June 2017

27

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21 June 2017

22

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21 June 2017

3117-3122

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Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

21 June 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

A graph-theory algorithm for rapid protein side-chain prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Protein design automation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Rotamer libraries in the 21st century

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Bayesian statistical analysis of protein side-chain rotamer preferences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Accurate bond and angle parameters for X-ray protein structure refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Modeling mutations in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

SPRINT: side-chain prediction inference toolbox for multistate protein design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Efficient rotamer elimination applied to protein side-chains and related spin glasses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Branch-and-terminate: a combinatorial optimization algorithm for protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Beyond rotamers: a generative, probabilistic model of side chains in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Configurational-bias sampling technique for predicting side-chain conformations in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

De novo protein design using pairwise potentials and a genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Solving and analyzing side-chain positioning problems using linear and integer programming

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Predicting protein mutant energetics by self-consistent ensemble optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Prediction of protein side-chain conformation by packing optimization.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Side-chain modeling with an optimized scoring function

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Practical conversion from torsion space to Cartesian space for in silico protein synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Protein structure prediction using Rosetta

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

A graph-theoretic algorithm for comparative modeling of protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

Depth-First Search and Linear Graph Algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

A new approach to the rapid determination of protein side chain conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

PISCES: a protein sequence culling server

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

The dead-end elimination theorem and its use in protein side-chain positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR538

10.1093/BIOINFORMATICS/BTR538

21 January 2018

Identifiers

DOI

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journals/bioinformatics/MiaoCJ11

21 June 2017

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DBLP Dataset 2021-01-02

28 January 2021

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