Journal ArticleDOI
Network analysis of protein structures identifies functional residues.
Gil Amitai,Arye Shemesh,Einat Sitbon,Maxim Shklar,Dvir Netanely,Ilya Venger,Shmuel Pietrokovski +6 more
TLDR
This work transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges, and found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values.About:
This article is published in Journal of Molecular Biology.The article was published on 2004-12-03. It has received 463 citations till now. The article focuses on the topics: Protein structure & Active site.read more
Citations
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Automated protein function prediction—the genomic challenge
TL;DR: The history of automated protein function prediction, a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows, and the latest innovations in all three topics are surveyed.
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A Network Representation of Protein Structures: Implications for Protein Stability
TL;DR: The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins, and could be crucial for the folding and stability of the unique three-dimensional structure of proteins.
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Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
TL;DR: ConCavity is introduced, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities and finds that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone.
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Residues crucial for maintaining short paths in network communication mediate signaling in proteins.
TL;DR: It is proposed that centrally conserved residues, whose removal increases the characteristic path length in protein networks, may relate to the system fragility.
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Predicting protein function from sequence and structural data.
TL;DR: Several automated servers that integrate evidence from multiple sources have been released this year and particular improvements have been seen with methods utilizing the Gene Ontology functional annotation schema.
References
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Journal ArticleDOI
A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease
TL;DR: The system used here indicates that only these sorts of substitution are capable of single-handedly reducing catalytic function to, or nearly to, levels that can be achieved by nonenzyme catalysts.
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In Vivo Characterization of Mutants of the Bacteriophage f1 Gene V Protein Isolated by Saturation Mutagenesis
TL;DR: The function of gene V protein mutants with single amino acid substitutions is tested by the ability of the mutant proteins to support phage growth, and by the inability of the proteins to inhibit the growth of Escherichia coli.
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Cation-dependent stability of subtilisin
TL;DR: It is shown that calcium binding at site B has relatively little effect on stability in the presence of moderate concentrations of monovalent cations, and this mutant of subtilisin BPN' which lacks calcium site A is examined.
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The ORFanage: an ORFan database
TL;DR: The ORFanage, an ORFan database, consists of the predicted ORFs in fully sequenced microbial genomes, and enables searching for the three types of ORFans in any subset of the genomes chosen by the user, which could help in choosing interesting targets for further genomic and evolutionary studies.
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Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.
TL;DR: Contrary to the prevalent view, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.