Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins (Q30430015)

14 October 2017

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

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14 October 2017

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1

Gerstein M

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14 October 2017

2

Levitt M

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14 October 2017

1 February 1998

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14 October 2017

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14 October 2017

7

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14 October 2017

2

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14 October 2017

445-456

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A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Optimum superimposition of protein structures: ambiguities and implications.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural 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=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Knowledge-based protein secondary structure assignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Understanding protein structure: using scop for fold interpretation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Effective protein sequence 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=2143933

Entrez: molecular biology database and retrieval system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Mapping the protein universe

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Protein structure comparison by alignment of distance matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Issues in searching molecular sequence databases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Protein superfamilies and domain superfolds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

The FSSP database of structurally aligned protein fold families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Derivation of rules for comparative protein modeling from a database of protein structure 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=2143933

Determinants of protein side-chain packing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

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=2143933

Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Insight into E-selectin/ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

The interpretation of protein structures: Estimation of static accessibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Improved tools for biological sequence 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=2143933

Protein structure 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=2143933

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and 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=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Selection of representative protein data sets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Structural comparisons of heme binding proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Volume changes in protein evolution.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Flexible algorithm for direct multiple alignment of protein structures and sequences.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

Gene duplications in H. influenzae.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143933

An Assessment of Amino Acid Exchange Matrices in Aligning Protein Sequences: The Twilight Zone Revisited

26 November 2018

1 reference

12 December 2020

Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers

1 reference

12 December 2020

Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains

1 reference

12 December 2020

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

1 reference

12 December 2020

Evolution of proteins formed by beta-sheets. I. Plastocyanin and azurin

1 reference

12 December 2020

Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures

1 reference

12 December 2020

A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database

1 reference

12 December 2020

SCOP: a Structural Classification of Proteins database

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

12 December 2020

How far can sequences diverge?

1 reference

12 December 2020

New structure--novel fold?

1 reference

12 December 2020

A polymerase I palm in adenylyl cyclase?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Multiple protein structure alignment

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

A polymerase I palm in adenylyl cyclase?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

A systematic approach to the comparison of protein structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Structural alignment of globins, phycocyanins and colicin A.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

The Protein Data Bank: a computer-based archival file for macromolecular structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Pfam: a comprehensive database of protein domain families based on seed alignments

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Algorithms on Strings, Trees, and Sequences

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Detection of common three-dimensional substructures in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

A solution for the best rotation to relate two sets of vectors

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Advances in comparative protein-structure modelling

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PRO.5560070226

Identifiers

DOI

10.1002/PRO.5560070226

1 reference

14 October 2017

1 reference

PMC publication ID

2143933

14 October 2017

PubMed publication ID

9521122

1 reference

PMC publication ID

2143933