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
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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
More filters
Journal ArticleDOI
An evolutionary trace method defines binding surfaces common to protein families
TL;DR: The evolutionary trace method is a systematic, transparent and novel predictive technique that identifies active sites and functional interfaces in proteins with known structure and provides an evolutionary perspective for judging the functional or structural role of each residue in protein structure.
Journal ArticleDOI
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
Fabian Glaser,Tal Pupko,Inbal Paz,Rachel E. Bell,Dalit Bechor-Shental,Eric Martz,Nir Ben-Tal +6 more
TL;DR: A new web server, ConSurf, is presented, which automates algorithms for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues.
Journal ArticleDOI
Requirement for integration of signals from two distinct phosphorylation pathways for activation of MAP kinase
TL;DR: It is demonstrated that MAP kinase is only active when both tyrosyl and threonyl residues are phosphorylated and suggested therefore that the enzyme functions in vivo to integrate signals from two distinct transduction pathways.