(Q36160842)

12 August 2017

Using protein design for homology detection and active site searches (English)

1 reference

12 August 2017

0 references

Nikolay V Dokholyan

2

0 references

Nick Grishin

series ordinal

4

object named as

Nick V Grishin

1 reference

PMCID

208762

12 August 2017

Eugene I. Shakhnovich

series ordinal

3

object named as

Eugene I Shakhnovich

1 reference

12 August 2017

Jimin Pei

1

1 reference

PMCID

208762

12 August 2017

language of work or name

English

0 references

publication date

15 September 2003

1 reference

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

12 August 2017

1 reference

12 August 2017

100

1 reference

12 August 2017

11361-11366

1 reference

12 August 2017

20

1 reference

Efficient biased estimation of evolutionary distances when substitution rates vary across sites

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Protein topology and stability define the space of allowed sequences.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Review: protein design--where we were, where we are, where we're going.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

AL2CO: calculation of positional conservation in a protein sequence alignment.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Native protein sequences are close to optimal for their structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

T-Coffee: A novel method for fast and accurate multiple sequence alignment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

De novo design and structural characterization of proteins and metalloproteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

SMART: a web-based tool for the study of genetically mobile domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Profile hidden Markov models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

SEALS: a system for easy analysis of lots of sequences.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

De novo protein design: fully automated sequence selection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Engineering of stable and fast-folding sequences of model proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

A new approach to the design of stable proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Crystal structure of CspA, the major cold shock protein of Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

A relationship between protein stability and protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

SCOP: a structural classification of proteins database for the investigation of sequences and structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Profile analysis: detection of distantly related proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Prediction of amino acid sequence from structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Protein design: a perspective from simple tractable models.

2 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Euclidian space and grouping of biological objects

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Combination of threading potentials and sequence profiles improves fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Structure prediction and active site analysis of the metal binding determinants in gamma -glutamylcysteine synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Protein threading using PROSPECT: design and evaluation.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=208762

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

23 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

Position-based sequence weights

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2034878100

21 January 2018

Identifiers

DOI

10.1073/PNAS.2034878100

1 reference

12 August 2017

0 references

1 reference

12 August 2017

1 reference

PMCID

208762