Description

This track shows alignments of sequences with known protein structures in the Protein Data Bank (PDB).

Display Conventions and Configuration

Genomic locations of PDB matches are labeled with the accession number. A click on them shows a standard feature detail page with the PDB page integrated into it. The protein structure is shown on the PDB page.

Methods

PDB sequences were downloaded from the PDB website and aligned with BLAST (tblastn). Only alignments with a minimum identity of 80% that span at least 80% of the query sequence were kept.

References

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. PMID: 10592235; PMC: PMC102472

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278