(Q35856225)

10 August 2017

Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements (English)

1 reference

10 August 2017

Victor Wai Tak Kam

1

1 reference

PMC publication ID

4692055

10 August 2017

William A Goddard

series ordinal

2

1 reference

10 August 2017

1 December 2008

1 reference

Journal of Chemical Theory and Computation

10 August 2017

1 reference

10 August 2017

4

1 reference

10 August 2017

12

1 reference

10 August 2017

2160-2169

1 reference

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

A hierarchical approach to all-atom protein loop prediction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

A de novo redesign of the WW domain

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Molecular recognition and docking algorithms

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Protein design is NP-hard

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Prediction of structure and function of G protein-coupled receptors

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Side-chain modeling with an optimized scoring function

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Extending the accuracy limits of prediction for side-chain conformations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Protein structure prediction.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Native protein sequences are close to optimal for their structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Automatic protein design with all atom force-fields by exact and heuristic optimization

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

The penultimate rotamer library

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Design, structure and stability of a hyperthermophilic protein variant

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Probing the role of packing specificity in protein design

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

De novo design of the hydrophobic cores of proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

WHAT IF: a molecular modeling and drug design program

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Computing van der Waals energies in the context of the rotamer approximation.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Computational design of a biologically active enzyme

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

Excluded volume in protein side-chain packing.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4692055

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

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26620487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein sidechain conformer prediction: a test of the energy function

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26620487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26620487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT800196K

1 reference

10 August 2017

1 reference

PMC publication ID

4692055

10 August 2017

PubMed publication ID

26620487

1 reference

PMC publication ID

4692055