(Q42750175)

6 November 2017

Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility (English)

1 reference

6 November 2017

1 reference

Atsushi Hijikata

1

1 reference

6 November 2017

Kei Yura

series ordinal

2

1 reference

6 November 2017

Tosiyuki Noguti

series ordinal

3

1 reference

6 November 2017

Mitiko Go

series ordinal

4

1 reference

6 November 2017

language of work or name

English

0 references

publication date

4 April 2011

1 reference

6 November 2017

1 reference

6 November 2017

79

1 reference

6 November 2017

6

1 reference

6 November 2017

1868-1877

1 reference

Protein-binding site prediction based on three-dimensional protein modeling.

6 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Improved prediction of protein side-chain conformations with SCWRL4

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

PSI-2: structural genomics to cover protein domain family space.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

The Universal Protein Resource (UniProt) 2009

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

PROMALS3D: a tool for multiple protein sequence and structure alignments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Understanding the molecular machinery of genetics through 3D structures

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Data growth and its impact on the SCOP database: new developments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Assessment of CASP7 predictions for template-based modeling targets

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Coverage of whole proteome by structural genomics observed through protein homology modeling database

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Comparative modeling for protein structure prediction

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

The impact of structural genomics: expectations and outcomes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

ProbCons: Probabilistic consistency-based multiple sequence alignment

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

MAFFT version 5: improvement in accuracy of multiple sequence alignment

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Protein homology detection by HMM-HMM comparison

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

MUSCLE: multiple sequence alignment with high accuracy and high throughput

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Announcing the worldwide Protein Data Bank

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Protein structure prediction and structural genomics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Evaluation of comparative protein structure modeling by MODELLER-3.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

A variable gap penalty function and feature weights for protein 3-D structure comparisons

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Amino acid substitution matrices from protein blocks

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Variable gap penalty for protein sequence-structure alignment

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

FORTE: a profile-profile comparison tool for protein fold recognition.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

PCMA: fast and accurate multiple sequence alignment based on profile consistency.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3110861

Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods

16 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.23011

SABmark--a benchmark for sequence alignment that covers the entire known fold space

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21465562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Relationship between mutability, polarity and exteriority of amino acid residues in protein evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21465562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21465562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.23011

1 reference

6 November 2017

1 reference

6 November 2017

PubMed publication ID

21465562

1 reference