(Q30353437)

20 June 2017

A machine learning information retrieval approach to protein fold recognition. (English)

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20 June 2017

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information retrieval

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2

Pierre Baldi

1 reference

20 June 2017

Jianlin Cheng

1

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PubMed ID

16547073

20 June 2017

language of work or name

English

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publication date

17 March 2006

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20 June 2017

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20 June 2017

22

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20 June 2017

12

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20 June 2017

1456-1463

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Basic local alignment search tool

20 June 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Score distributions for simultaneous matching to multiple motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Hidden Markov models of biological primary sequence information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

An empirical energy function for threading protein sequence through the folding motif

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

3D-1D threading methods for protein fold recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Establishing homologies in protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Profile hidden Markov models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

COACH: profile-profile alignment of protein families using hidden Markov models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

A study of combined structure/sequence profiles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

3D-Jury: a simple approach to improve protein structure predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Amino acid substitution matrices from protein blocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Hidden Markov models for sequence analysis: extension and analysis of the basic method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Fold prediction by a hierarchy of sequence, threading, and modeling methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

A new approach to protein fold recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

A neural network approach to evaluate fold recognition results.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Hidden Markov models for detecting remote protein homologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Enhanced genome annotation using structural profiles in the program 3D-PSSM

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

PROSPECT II: protein structure prediction program for genome-scale applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Hidden Markov models in computational biology. Applications to protein modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Identification of related proteins on family, superfamily and fold level.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Pcons: a neural-network-based consensus predictor that improves fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

A comparison of profile hidden Markov model procedures for remote homology detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Alignment of protein sequences by their profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

3DCoffee: combining protein sequences and structures within multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Combination of threading potentials and sequence profiles improves fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Improved tools for biological sequence comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Improving sequence-based fold recognition by using 3D model quality assessment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Protein fold recognition by prediction-based threading

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Identification of common molecular subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Protein homology detection by HMM-HMM comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Sequence alignment and penalty choice. Review of concepts, case studies and implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Using evolutionary information for the query and target improves fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Scoring profile-to-profile sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

An efficient computational method for globally optimal threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTL102

10.1093/BIOINFORMATICS/BTL102

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/ChengB06

20 June 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

16547073