ProtCID
Encyclopedia
The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces
in crystal structures of homologous proteins.
Its main goal is to identify and cluster homodimeric
and heterodimeric interfaces observed in multiple crystal forms of homologous proteins. Such interfaces, especially of non-identical proteins or protein complexes, have been associated with biologically relevant interactions.
A common interface in ProtCID indicates chain-chain interactions that occur in different crystal forms. All protein sequences of known structure in the Protein Data Bank
(PDB) are assigned a ”Pfam
chain architecture”, which denotes the ordered Pfam assignments for that sequence, e.g. (Pkinase) or (Cyclin_N)_(Cyclin_C). Homodimeric interfaces in all crystals that contain a particular architecture are compared, regardless of whether there are other protein types in the crystals. All interfaces between two different Pfam architectures in all PDB entries that contain them are also compared (e.g., (Pkinase) and (Cyclin_N)_(Cyclin_C) ). For both homodimers and heterodimers, the interfaces are clustered into common interfaces based on a similarity score.
ProtCID reports the number of crystal forms that contain a common interface, the number of PDB entries, the number of PDB and PISA biological assembly annotations that contain the same interface, the average surface area, and the minimum sequence identity of proteins that contain the interface. ProtCID provides an independent check on publicly available annotations of biological interactions for PDB entries.
Protein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
in crystal structures of homologous proteins.
Its main goal is to identify and cluster homodimeric
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...
and heterodimeric interfaces observed in multiple crystal forms of homologous proteins. Such interfaces, especially of non-identical proteins or protein complexes, have been associated with biologically relevant interactions.
A common interface in ProtCID indicates chain-chain interactions that occur in different crystal forms. All protein sequences of known structure in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
(PDB) are assigned a ”Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
chain architecture”, which denotes the ordered Pfam assignments for that sequence, e.g. (Pkinase) or (Cyclin_N)_(Cyclin_C). Homodimeric interfaces in all crystals that contain a particular architecture are compared, regardless of whether there are other protein types in the crystals. All interfaces between two different Pfam architectures in all PDB entries that contain them are also compared (e.g., (Pkinase) and (Cyclin_N)_(Cyclin_C) ). For both homodimers and heterodimers, the interfaces are clustered into common interfaces based on a similarity score.
ProtCID reports the number of crystal forms that contain a common interface, the number of PDB entries, the number of PDB and PISA biological assembly annotations that contain the same interface, the average surface area, and the minimum sequence identity of proteins that contain the interface. ProtCID provides an independent check on publicly available annotations of biological interactions for PDB entries.