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ProtCAD database can be searched by PDB ID, Pfam ID (accession code) and UniProt ID (accession code).


  • PDB ID

    Input a PDB ID to find all assemblies in the entry and their Pfam architectures and clusters.  

    PDB 4dsn

    Column Annotation
    Assembly ID The integer number of an assembly of this entry
    Symmetry The symmetry of an assembly
    Stoichiometry The stoichiometry of an assembly
    CF ID The string ID for crystal form
    (UniProt)n The UniProt component of an assembly
    Arch Pfam architecture
    (Arch)n The Pfam architecture composition of a cluster with copy numbers
    Group ID The integer number of a Pfam architecture
    Cluster ID The integer number of a cluster
    CF_clus The number of CFs in a cluster
    ENT_clus The number of PDB entries in a cluster
    UNP_clus The number of UniProts in a cluster
    Seq_Identity The minimum sequence identity of a cluster

    Click Pfam architecture group ID ("GroupID") returns all assemblies in the group.

    Assemblies in Ras

    Click the link "Assembly Clusters" goes to the clusters page.

    Ras Clusters


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  • Pfam ID

    Input a Pfam ID to find all Pfam architectures containing the Pfam.

    Pfam UDG

    Column Annotation
    Group ID The integer number of a Pfam architecture
    Arch Pfam architecture
    Cluster ID The integer number of a cluster
    Symmetry The symmetry of an assembly
    Stoichiometry The stoichiometry of an assembly
    SeqID The minimum sequence identity of protein sequences in a cluster/td>
    CF_clus The number of CFs in a cluster
    CF_arch The number of CFs in a Pfam architecture
    R_CF The ratio between CF_clus and CF_arch
    CF_UNPclus The number of CFs of all UniProts in a cluster
    CF_UNParch The number of CFs of the same UniProts of the cluster in the Pfam architecture
    R_CF_UNPclus The ratio between CF_UNPclus and CF_UNParch
    UNP_clus The number of UniProts in a cluster
    UNP_arch The number of UniProts in a Pfam architecture
    R_UNP The ratio between UNP_clus and UNP_pdb
    ENT_clus The number of PDB entries in a cluster
    ENT_arch The number of PDB entries in a Pfam architecture
    R_ENT The ratio between ENT_clus and ENT_arch
    PDBBA The number of PDB entries containing biological assemblies same as the cluster assembly
    R_PDB The ratio between PDBBA and ENT_clus
    EPPICBA The number of PDB entries containing EPPIC predicted biological assemblies same as the cluster assembly
    R_EPPIC The ratio between EPPICBA and ENT_clus
    PISABA The number of PDB entries containg PISA predicted biological assemblies same as the cluster assembly
    R_PISA The ratio between PISABA and ENT_clus
    (Arch)n The Pfam architecture composition of a cluster with copy numbers

    Click a Pfam architecture group id returns the clusters.

    (UDG) clusters


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  • UniProt code

    Input a UniProt code to find all assembly clusters containing the input UniProt.

    (UDG) clusters

    Column Annotation
    Group ID The integer number of a Pfam architecture group
    Arch Pfam architecture
    The following rows are about a cluster
    Cluster ID The integer number of an assembly cluster
    Symmetry The symmetry of an assembly
    Stoichiometry The stoichiometry of an assembly
    SeqID The minimum sequence identity of protein sequences in a cluster/td>
    CF_clus The number of crystal forms in a cluster
    CF_arch The number of crystal forms in a Pfam architecture
    R_CF The ratio between CF_clus and CF_arch
    ENT_clus The number of PDB entries in a cluster
    ENT_arch The number of PDB entries in a Pfam architecture
    R_ENT The ratio between ENT_clus and ENT_arch
    The following columns are numbers about the input UniProt in a cluster and in a Pfam architecture
    CF_UNP_clus The number of crystal forms of the input UniProt in a cluster
    CF_UNP_arch The number of crystal forms of the input UniProt in a Pfam architecture
    R_CF_UNP_clus The ratio between CF_UNP_clus and CF_UNP_arch
    ENT_UNP_clus The number of PDB entries containing the input UniProt in a cluster
    ENT_UNP_arch The number of PDB entries containing the input UniProt in a Pfam architecture
    R_ENT_UNP_clus The ratio between ENT_UNP_clus and ENT_UNP_arch
    PDBBA_UNP_clus The number of PDB entries containing the input UniProt having at least one PDB biological assembly in the cluster
    R_PDB The ratio between PDBBA_UNP_clus and ENT_UNP_clus
    PISABA_UNP_clus The number of PDB entries containing the input UniProt having PISA predicted assemblies in the cluster
    R_PISA The ratio between PISABA_UNP_clus and ENT_UNP_clus
    EPPICBA_UNP_clus The number of PDB entries containing the input UniProt having EPPIC predicted biological assemblies in the cluster
    R_EPPIC The ratio between EPPICBA_UNP_clus and ENT_UNP_clus

    Click the link "Click here for Assemblies containing EGFR_HUMAN" on the UniProt clusters page returns all assemblies containing the input UniProt.

    EGFR assemblies


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