TY - JOUR
T1 - The protein common interface database (ProtCID)-A comprehensive database of interactions of homologous proteins in multiple crystal forms
AU - Xu, Qifang
AU - Dunbrack, Roland L.
PY - 2011/1
Y1 - 2011/1
N2 - 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 theprotein 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. Thesame 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 allinterfaces in a cluster are downloadable for further analysis. ProtCiD is available at http://dunbrack2. fccc.edu/protcid.
AB - 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 theprotein 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. Thesame 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 allinterfaces in a cluster are downloadable for further analysis. ProtCiD is available at http://dunbrack2. fccc.edu/protcid.
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U2 - 10.1093/nar/gkq1059
DO - 10.1093/nar/gkq1059
M3 - Article
C2 - 21036862
SN - 0305-1048
VL - 39
SP - D761-D770
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -