PDB ID [PDB ID] A PDB ID is a unique 4-character code for each entry in the Protein Data Bank. The first character must be a number between 1 and 9, and the remaining three characters can be letters or numbers. |
BLAST BLAST stands for Basic Alignment Search Tool. Because of its speed and the reliability, BLAST is a very widely used program for sequence alignment. The statistical significance of a BLAST alignment is given by its expectation value or E-value. The E-value ... |
MAFFTash MAFFTash URL: http://sysimm.org/MAFFTash// - Overview - Usage - Methods - Structural alignment Sequence alignment - Structural alignment - Sequence alignment - Prep-MAFFTash - MAFFTash Output - References [Overview] MAFFTash is a server that ... |
PDBML-extatom PDBML-extatom files contain atomic coordinates in a "simplified" format. The XML schema for PDBML-extatom format is provided at: - https://pdbj.org//schema/pdbx-v40-ext.xsd And can also be viewed using our interactive XML viewer. In the canonical PDBML ... |
SeSAW Tutorial In this tutorial, we provide explanation about the SeSAW, one of the service of PDBj. See also the SeSAW documentation about basic things such as used technique. - Submitting PDB entries to SeSAW - Submitting structures to SeSAW - Experimental ... |
structural domain A structural domain is a level of organization that is intermediate between secondary structure and tertiary structure. For single domain structures, a structural domain can be thought of as being equivalent to the tertiary structure, with the caveat that ... |
Functional annotation example [Functional Annotation of] 1uan 1uan (TT1542 from Thermus thermophilus HB8) is a structural genomics (SG) target solved as part of the Protein 3000 project in Japan [1]. At the time the structure was solved, there were no PDB entries with significant ... |
Structure Prediction - CRNPRED (Structure prediction service based on the sequence) - Spanner (Structure prediction service using structure known molecules with similar sequence) - SFAS (Multiple service both sequence alignment and structure prediction) [CRNPRED] CRNPRED is ... |
eProtS [Encyclopedia of Protein Structures] https://pdbj.org//eprots/ The eProtS, Encyclopedia of Protein Structure, is a dictionary with pictures of the protein three-dimensional structures, for understanding the tertiary structures and the biological ... |
Sequence Navigator URL: https://pdbj.org/seqNavi [Overview] Sequence Navigator is a BLAST interface to PDBj. The input to Sequence Navigator can be a PDB ID or an amino acid sequence. The output is a set of BLAST alignments to homologous PDB entries. There are options for ... |
jV Web page : https://pdbj.org//jv/index.html Original Manual in English : http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Japanese version with some usage example : https://pdbj.org//jv/manual/index_ja.html Help page in English : http://ef-site.hgc.jp/ ... |
tyr |
trp |
val |
thr |
ser |
arg |
gln |
pro |
asn |
met |
leu |
lys |
ile |
his |