In this issue

Open Mass Spectrometry Search Algorithm (OMSSA)

Probe Database Debut

New Structure Link from Protein

BLAST Download Update

New Microbial Genomes in GenBank

Nucleotide Database Splits

NCBI 4-Pack Course

RefSeq Release 14

New Organisms in UniGene

GenBank Passes 100 Gigabases

New BLAST Formatter

Splign Alignment Tool

GenBank Release 150

New Genome Builds

Submission Corner


New Related Structures Link from Proteins in Entrez

One of the first steps in modeling the 3D structure of a protein is to find solved structures of proteins that have a high degree of sequence similarity to a target sequence. Because only about 1% of the protein sequences in the Entrez protein database are derived from protein structures, it will usually be necessary to find sequence-related structures in order to link a protein to a 3D structure. Entrez now displays new Related Structures links that perform this function with a single click of the mouse. Each protein sequence in Entrez Protein that has a BLAST hit to a structure-derived sequence now has a Related Structure link in the Links menu to the right of the record in the Entrez display; almost 36% of the 7.3 million protein sequences in Entrez have such links. Following this link displays the BLAST alignments of the related structures to the query either graphically or as a table, and these results can be sorted by BLAST score, E-value, aligned length, or sequence identity. Clicking on any of the alignment bars displays a detailed pairwise alignment and allows the alignment to be loaded into Cn3D for viewing. Figure 1 displays the non-identical related structures to NP_690059, the NCBI RefSeq for coagulation factor VII in rat. Sequence-similar structures align to both the catalytic heavy chain and the calcium-binding light chain of the protein. Figure 2 shows alignment of the query to 1KLI_H, the heavy chain of the human homolog displayed in Cn3D.

Figure 1. The Entrez links menu for the NCBI RefSeq for rat coagulation factor VII showing the "Related Structure" link. This link leads to the graphical display of alignments of sequence-similar proteins from the structure database. Clicking on the graphic alignment with 1KLH_H displays the sequence alignment that can then be mapped onto the structure using Cn3D.

Figure 2. Cn3D display of the human coagulation factor VII heavy chain, 1KLI_H colored by the sequence alignment with the rate RefSeq, NP_690059. This mapping of the residues of the rat protein onto the human structure can be used in the construction of a structural model for the rat protein.


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NCBI News | Fall/Winter 2002 NCBI News: Spring 2003