Help and documentation

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  • Overview

    ProtCID is comprehensive database of interactions of protein-protein and protein-other molecules. It fuses different data sources, computes interactions in PDB crystals at protein and domain levels, clusters interactions across homologous proteins. ProtCID clusters can identify biological relevant interactions, especially these weak dimers that may not be readily apparent even to experienced structural biologists. ProtCID clusters can be used to generate hypotheses by extending existing experimental data on some proteins to many other proteins in the same cluster, family and clan. ProtCID clusters can be used to identify structural information for multi-protein complexes and hub proteins.

  • Search

    ProtCID can searched by PDB ID, one Pfam, a Pfam pair, one sequence, two sequences, one UniProt and a list of UniProts.

  • Browse

    Pfams, Clans, Pfam pairs, peptide binding Pfams and ligands can be browsed.

  • PyMOL script

    PyMol scripts are provided to visualize chain and domain interface clusters, Pfam domains, Pfam-peptide interfaces and their clusters, and Pfam-ligand interactions and their clusters. Chains and domains are aligned by Pfam hidden Markov models and structures.

  • Download

    All coordinates of interfaces, interactions, clusters can be downloaded. Sequences and clusters text files can also be downloaded.

  • UniProts Input

    ProtCID can be searched by one Uniprot or a list of UniProts, and returns Pfams of each Uniprot and interactions based on the crystals of the input proteins or the crystals of homolgous proteins containing same Pfams.

  • Pfam-peptide Interfaces

    Peptide binging Pfams can be browsed. ProtCID provides a list of Professional Peptide Binding Domains (PPBDs) which means the function of Pfam domains is to bind peptides. A PPBD is defined as a Pfam containing at least 3 human proteins that bind peptides in the PDB, but excluding those enzymes and repeats. In the table of peptide binding Pfams, the last column ("Is PPBD") shows whether the Pfam is a PPBD("Y" or "N"). It can be sorted so the list of PPBDs can be browsed.

  • Pfam-ligand Interactions

    ProtCID provides two types of Pfam-ligand interactions: A Pfam and its interacting ligands (e.g. SH3_2.tar.gz), a ligand and its interacting Pfams (e.g. DNA.tar.gz).

  • Pfam Interaction Networks

    There are two types of Pfam interaction networks: A Pfam and its interacting Pfams, Pfam-Pfam interaction networks.

  • Glossary

    The important terms used in ProtCID are explained here.