(Q31034795)

1 September 2017

Side-chain modeling with an optimized scoring function (English)

1 reference

1 September 2017

2

Nick V Grishin

1 reference

1 September 2017

Shide Liang

1

1 reference

1 September 2017

1 February 2002

1 reference

1 September 2017

1 reference

1 September 2017

11

1 reference

1 September 2017

322-331

1 reference

1 September 2017

2

1 reference

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

1 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

21 June 2018

Extending the accuracy limits of prediction for side-chain conformations

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

The penultimate rotamer library

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

21 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Bayesian statistical analysis of protein side-chain rotamer preferences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Automated design of the surface positions of protein helices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Determination of atomic desolvation energies from the structures of crystallized proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Modeling side-chain conformation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Ligand-protein docking and rational drug design.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Prediction of protein side-chain conformation by packing optimization.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Computational method for the design of enzymes with altered substrate specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373451

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

21 June 2018

1 reference

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

21 January 2018

1 reference

Side-chain prediction by neural networks and simulated annealing optimization.

21 January 2018

1 reference

Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.

21 January 2018

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

A Simplex Method for Function Minimization

21 January 2018

1 reference

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

21 January 2018

1 reference

12 December 2020

A method to configure protein side-chains from the main-chain trace in homology modelling

1 reference

12 December 2020

Protein sidechain conformer prediction: a test of the energy function

1 reference

12 December 2020

Determinants of side chain conformational preferences in protein structures

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.24902

1 reference

1 September 2017

1 reference

1 September 2017

1 reference

PMCID

2373451