(Q46972510)

27 December 2017

title

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

1 reference

27 December 2017

0 references

1 reference

0 references

3

1 reference

27 December 2017

author name string

Sauder JM

series ordinal

1

1 reference

27 December 2017

Arthur JW

series ordinal

2

1 reference

27 December 2017

language of work or name

English

0 references

publication date

1 July 2000

1 reference

27 December 2017

published in

Proteins

1 reference

27 December 2017

volume

40

1 reference

27 December 2017

issue

1

1 reference

27 December 2017

page(s)

6-22

1 reference

27 December 2017

Knowledge-based prediction of protein structures and the design of novel molecules

cites work

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Comparative modeling methods: application to the family of the mammalian serine proteases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Comparative protein modelling by satisfaction of spatial restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Model for haptoglobin heavy chain based upon structural homology

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Identification of common molecular subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

A new approach to protein fold recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Protein fold recognition using sequence-derived predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Intermediate sequences increase the detection of homology between sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Combining sensitive database searches with multiple intermediates to detect distant homologues

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Profile analysis: detection of distantly related proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Rapid and sensitive sequence comparison with FASTP and FASTA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Local alignment statistics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Hidden Markov models for detecting remote protein homologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

CATH--a hierarchic classification of protein domain structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

A comprehensive comparison of multiple sequence alignment programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

A surface of minimum area metric for the structural comparison of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Dali: a network tool for protein structure comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

SSAP: sequential structure alignment program for protein structure comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Optimum superimposition of protein structures: ambiguities and implications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

The structural alignment between two proteins: is there a unique answer?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Derivation of rules for comparative protein modeling from a database of protein structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Touring protein fold space with Dali/FSSP

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

SCOP: a Structural Classification of Proteins database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

The FSSP database: fold classification based on structure-structure alignment of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

A data bank merging related protein structures and sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Using CLUSTAL for multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Homology-based fold predictions for Mycoplasma genitalium proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Protein folds and families: sequence and structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

MMDB: Entrez's 3D structure database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Genome analysis: Assigning protein coding regions to three-dimensional structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Fold and function predictions for Mycoplasma genitalium proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Non-globular domains in protein sequences: automated segmentation using complexity measures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Knowledge-based protein secondary structure assignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

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/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000701%2940%3A1%3C6%3A%3AAID-PROT30%3E3.0.CO%3B2-7

10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7

21 January 2018

Identifiers

DOI

1 reference

27 December 2017

1 reference

27 December 2017