The protein common interface database (ProtCID)—a comprehensive database of interactions of homologous proteins in multiple crystal forms
Qifang Xu,Roland L. Dunbrack +1 more
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TLDR
By examining interfaces that are shared by many homologous proteins in different CFs, it is found that the PDB and the Protein Interfaces, Surfaces, and Assemblies (PISA) are not always consistent in their annotations of biological assemblies in a homologueous family.Abstract:
The protein common interface database (ProtCID) is a database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). Such interfaces, especially of homologous but non-identical proteins, have been associated with biologically relevant interactions. In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. For a single PFAM architecture, all the dimers present in each CF are constructed and compared with those in other CFs that contain the same domain architecture. Interfaces occurring in two or more CFs comprise an interface cluster in the database. The same process is used to compare heterodimers of chains with different domain architectures. By examining interfaces that are shared by many homologous proteins in different CFs, we find that the PDB and the Protein Interfaces, Surfaces, and Assemblies (PISA) are not always consistent in their annotations of biological assemblies in a homologous family. Our data therefore provide an independent check on publicly available annotations of the structures of biological interactions for PDB entries. Common interfaces may also be useful in studies of protein evolution. Coordinates for all interfaces in a cluster are downloadable for further analysis. ProtCiD is available at http://dunbrack2.fccc.edu/protcid.read more
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Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
Martino Bertoni,Martino Bertoni,Florian Kiefer,Florian Kiefer,Marco Biasini,Marco Biasini,Lorenza Bordoli,Lorenza Bordoli,Torsten Schwede,Torsten Schwede +9 more
TL;DR: A description of protein-protein interface conservation as a function of evolutionary distance to reduce the noise in deep multiple sequence alignments and a distance measure to structurally compare homologous multimeric protein complexes are defined.
Journal ArticleDOI
Predicting Protein-Protein Interactions from the Molecular to the Proteome Level
TL;DR: This review aims to provide a background on PPIs and their types and list the state-of-the-art methods, servers, databases, and tools for protein-protein interaction prediction.
Journal ArticleDOI
iPfam: a database of protein family and domain interactions found in the Protein Data Bank
TL;DR: The iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database, allowing for independent development, improving data access and giving clearer separation between the protein family and interactions datasets.
Journal ArticleDOI
Protein interface classification by evolutionary analysis
TL;DR: A protein-protein interface classifier that relies on evolutionary data to detect the biological character of interfaces and it is demonstrated that a more conservative selection of homolog sequences - with relatively high sequence identities to the query - is able to produce a clearer signal than previous attempts.
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