Structural Genomics (SG) refers to the structural determination of all the proteins in a particular genome. More generally, SG has come to mean the effort to solve a representative set of protein structures, from which models of all proteins can be built ...

http://bmrbdep.pdbj.org/index_en.html BMRB is a database for NMR data of peptides, proteins and nucleic acids, and is maintained by BioMagResBank at the University of Wisconsin-Madison. This website is maintained by PDBj-BMRB group at Institute for ...

URL： https://pdbj.org//spanner/ Spanner is a structural homology modeling program―that is, it threads a specific amino-acid sequence onto a specific PDB structure, patching up the gaps as best it can. To create a model, you must provide a template ...

[Contents] - Contents - URL - What is CRNPRED? - How to use CRNPRED server - How should I interpret the results? I don't receive any email from CRNPRED! - How should I interpret the results? - I don't receive any email from CRNPRED! - How CRNPRED ...

Sequence representative lists are generated by first computing BLAST scores for all pairs of structures. The pairs which score above a certain threshold (Sequence identity30% and E-value0.1) arelinked. The set is first clustered using single-linkage ...

[NER] NER stands for the Number of Equivalent Residues [1] is an empirical measure of the similarity of two protein structures. The NER superposition corresponds to the rotation and translation that maximizes the NER score. The NER score is bounded ...

RMSD stands for root mean square deviation. It is a commonly used measure of dissimilarity or error in protein structure. For two sets of points and a mapping between those points the RMSD is defined to be the square-root of the average of the squared ...

[Alignment] In bioinformatics, alignment refers to a mapping betweenequivalentamino acids (in the case of proteins) or nuceotides (in the case of DNA or RNA). In the case of proteins, we usually consider two basic types of alignment, sequence alignment ...

[Structural Superposition] The term structural superposition refers to rotations and translations performed on one molecular structure to make it match another structure or structures. Inherent in the definition of structural superposition is an assumed ...

[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 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 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 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 ...

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 ...

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 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 ...

- 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 ...

[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 ...

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 ...

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/ ...