(Q30408153)

5 September 2017

Using structure to explore the sequence alignment space of remote homologs (English)

1 reference

5 September 2017

1 reference

Andrew Kuziemko

1

1 reference

5 September 2017

Barry Honig

series ordinal

2

1 reference

5 September 2017

Donald Petrey

series ordinal

3

1 reference

5 September 2017

6 October 2011

1 reference

PLOS Computational Biology

5 September 2017

1 reference

5 September 2017

7

1 reference

5 September 2017

10

1 reference

5 September 2017

e1002175

1 reference

Creative Commons Attribution 4.0 International

5 September 2017

start time

6 October 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Critical assessment of methods of protein structure prediction-Round VII

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Sequence alignments in the neighborhood of the optimum with general application to dynamic programming

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

On the origin and highly likely completeness of single-domain protein structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Fragnostic: walking through protein structure space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

The protein structure prediction problem could be solved using the current PDB library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Protein homology detection by HMM-HMM comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Scoring function for automated assessment of protein structure template quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Alignment of protein sequences by their profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

A comparison of scoring functions for protein sequence profile alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Comparative protein structure modeling by iterative alignment, model building and model assessment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

In search for more accurate alignments in the twilight zone

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Powers and pitfalls in sequence analysis: the 70% hurdle

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

20 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=3188491

Twilight zone of protein sequence alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Assessing protein structures with a non-local atomic interaction energy.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

VERIFY3D: assessment of protein models with three-dimensional profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Threading a database of protein cores

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Protein fold recognition by mapping predicted secondary structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

Evaluation and improvements in the automatic alignment of protein sequences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

A simple method to generate non-trivial alternate alignments of protein sequences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

A new approach to protein fold recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188491

The PDB is a covering set of small protein structures

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Variable gap penalty for protein sequence-structure alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Combination of threading potentials and sequence profiles improves fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Large-scale comparison of protein sequence alignment algorithms with structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

The crystal structure of E.coli 1-deoxy-D-xylulose-5-phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and NADPH reveals a tight-binding closed enzyme conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Estimating quality of template-based protein models by alignment stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Some biological sequence metrics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Fold recognition by concurrent use of solvent accessibility and residue depth

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002175

Distribution of Indel lengths

21 January 2018

1 reference

12 December 2020

Alignment of the amino acid sequences of distantly related proteins using variable gap penalties

1 reference

12 December 2020

On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles

1 reference

12 December 2020

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002175

Identifiers

DOI

1 reference

journals/ploscb/KuziemkoHP11

5 September 2017

1 reference

DBLP Dataset 2021-01-02

release_sauvmrvmhfb4rdfhh3mnypwn4m

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/sauvmrvmhfb4rdfhh3mnypwn4m

24 November 2022

mapped directly with Wikidata item

1 reference

5 September 2017

PubMed publication ID

21998567

1 reference