Improved recognition of native-like protein structures using a family of designed sequences (Q30329384)

13 September 2017

Improved recognition of native-like protein structures using a family of designed sequences (English)

1 reference

13 September 2017

0 references

2

Michael Levitt

1 reference

13 September 2017

Patrice Koehl

1

0 references

language of work or name

English

0 references

publication date

8 January 2002

1 reference

Proceedings of the National Academy of Sciences of the United States of America

13 September 2017

1 reference

13 September 2017

99

1 reference

13 September 2017

691-696

1 reference

13 September 2017

2

1 reference

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Ab initio construction of protein tertiary structures using a hierarchical approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Effective energy functions for protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Comparison of sequence profiles. Strategies for structural predictions using sequence information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

De novo protein design. I. In search of stability and specificity.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Ab initio protein structure prediction of CASP III targets using ROSETTA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Twilight zone of protein sequence alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Protein structure prediction by threading. Why it works and why it does not.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Coupling the folding of homologous proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Predicting protein structure using hidden Markov models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Statistical mechanics of simple models of protein folding and design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Mean-field minimization methods for biological macromolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Potential energy functions for threading

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Engineering of stable and fast-folding sequences of model proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

A new approach to the design of stable proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Potential energy functions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Principles that govern the folding of protein chains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

The relation between the divergence of sequence and structure in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

The SWISS-PROT protein sequence data bank

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Database of homology-derived protein structures and the structural meaning of sequence alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

A new approach to protein fold recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Assessment of protein models with three-dimensional profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Topology fingerprint approach to the inverse protein folding problem

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Amino acid substitution matrices from protein blocks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Protein tertiary structure recognition using optimized Hamiltonians with local interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117367

Equation of State Calculations by Fast Computing Machines

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

A global geometric framework for nonlinear dimensionality reduction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Correctly folded proteins make twice as many hydrophobic contacts

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Progress in protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Factors affecting the ability of energy functions to discriminate correct from incorrect folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

How homologs can help to predict protein folds even though they cannot be predicted for individual sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Polar and nonpolar atomic environments in the protein core: implications for folding and binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Determinants of a protein fold. Unique features of the globin amino acid sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

De novo protein design. II. Plasticity in sequence space

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.022408799

Sequence and structure conservation in a protein core

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11782533

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.022408799

1 reference

13 September 2017

0 references

1 reference

13 September 2017

1 reference

PMCID

117367