An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

Srinivasan, N.; Blundell, Tom L.

doi:10.1093/protein/6.5.501

Cited by 120Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

Srinivasan, N., Blundell, Tom L.·1993·"Protein Engineering, Design and Selection"

DOI 10.1093/protein/6.5.501

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Abstract

A 3-D model of a protein can be constructed from its amino acid sequence and the 3-D structures of one or more homologues by annealing three sets of fragments: the structurally conserved regions, structurally variable regions and the side chains. The method encoded in the computer program COMPOSER was assessed by generating 3-D models of eight proteins whose crystal structures are already known and for which 3-D structures of homologues are available. In the structurally conserved regions, differences between modelled and X-ray structures are smaller than the differences between the X-ray structures of the modelled protein and the homologues used to build the model. When several homologues are used, the contributions of the known structures are weighted, preferably by the square of sequence similarity; this is especially important when the similarities of the homologues to the modelled structure differ greatly. The 'collar' extension approach, in which a similar region of different length in a homologue is used to extend the framework, can result in a more accurate model. If known homologues comprise more than one related group of proteins and they are both distantly related to the unknown, then alignment of the sequence to be modelled with each group of homologues facilitates identification of structurally conserved regions of the unknown and leads to an improved model. Models have root mean square differences (r.m.s.d.s) with the structures defined by X-ray analysis of between 0.73 and 1.56 A for all C alpha atoms, for seven the eight models. For the model of mucor pepsin, where the closest homologue has 33% sequence identity and 20% of the residues are in structurally variable regions, the r.m.s.d. for the framework region is 1.71 A and the r.m.s.d. for all C alpha atoms is 3.47 A.

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The domains presented were the consensus of folds identified by Composer, MatchMaker, GeneFold, Robetta, Fugue, and Swiss-Model.
“The domains presented were the consensus of folds identified by Composer [53], MatchMaker [54], GeneFold [55], Robetta [56], Fugue [57], and Swiss-Model [58].”
From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [53]

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Authors: Srinivasan, N., & Blundell, T. L.
Affiliations: University of London (GB)
Birkbeck, University of London (GB)
ORCID: Srinivasan, N.
Blundell, Tom L.
Venue: "Protein Engineering, Design and Selection"
Publisher: Oxford University Press (OUP)
Published: 1993
Volume: 6
Issue: 5
Pages: 501-512
ISSN: 0269-2139 (ISSN-L)
1741-0126
1741-0134
DOI: 10.1093/protein/6.5.501
OpenAlex: W2053449148
Cited by: 119
References: 0
Citations by year: 2024: 1 · 2023: 1 · 2022: 1 · 2021: 2 · 2020: 2 · 2018: 1 · 2017: 2 · 2016: 5 · 2015: 1 · 2014: 3 · 2013: 1 · 2012: 1
FWCI: 2.45
Type: journal article
Language: en
Open access: closed
Locations: Protein Engineering Design and Selection (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Keywords: protein tertiary structure, homology modeling, composer, model accuracy assessment, RMSD
MeSH terms: Amino Acid Sequence, Azurin, Computer Simulation, Elapid Venoms, Evaluation Studies as Topic, Models, Molecular, Molecular Sequence Data, Muramidase, Myoglobin, Pepsin A, Software, Trypsin, Reproducibility of Results, Aspartic Acid Endopeptidases, Sequence Homology, Amino Acid, Protein Structure, Tertiary

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An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

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