iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions

By Robert D. Finn, Mhairi Marshall, Alex Bateman. Bioinform., 2005

315 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/976bf831c93db63fabe4a8f7826d357b013115e4

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments (2010, methodology): “For each Pfam alignment, all corresponding PDB files were collected according to the iPfam annotation [36] and distances between pairs of residues were determined as the distance between the C b atoms ( C a for glycines).”
In silico prediction of protein-protein interactions in human macrophages (2001, background): “Identifies whether the interactors pair contains domains known as interacting according to the Pfam database [44].”
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, methodology): “Domain interactions are automatically derived from various data sources and interactions potentially disrupted by alternative splicing according to the AltAnalyze results can be readily identiﬁed (Figure 3D, domain interactions obtained from iPfam; 29).”
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis (2013, methodology): “After that all known interacting domain pairs, as available from 3DID (26), and iPFAM (27), were removed.”
Protein–protein interaction and quaternary structure (2008, background): “Classical examples are the immunoglobulin domains or the Sarc homology SH2 and SH3 domains, but databases such as InterPro (Apweiler et al. 2001), PFAM and its derivative iPFAM (Finn et al. 2005) list thousands more.”
Recent progress and future directions in protein-protein docking. (2008, methodology): “Using a coarse FFT grid implies using low order correlations and also serves to soften the potential [46].”
Pfam: clans, web tools and services (2005, background): “An additional feature, iPfam (a sister database containing details of Pfam domain‐domain interactions) has been described in a recent publication ( 3 ).”
Three-dimensional reconstruction of protein networks provides insight into human genetic disease (2012, methodology): “We used both iPfam 17 and 3did 18 to identify the interfaces of two interacting proteins by mapping them to known atomic-resolution 3D structures of interactions in the Protein Data Bank (PDB) 19 ( Fig.”