3d-blast.life.nctu.edu.tw
3D-BLAST E-value
http://3d-blast.life.nctu.edu.tw/evalue.php
3d-blast.life.nctu.edu.tw
3D-BLAST Download
http://3d-blast.life.nctu.edu.tw/download.php
You download the package from:. Standalone 3d-blast Linux beta102.tar.gz. Standalone 3d-blast Mac beta102.tar.gz. Standalone 3d-blast Mac beta102 Lion.tar.gz. After downloading the package to you Linux-based computer, uncompress it by following commands in terminal. Gunzip Standalone 3d-blast Linux beta102.tar.gz. Tar -xpf Standalone 3d-blast Linux beta102.tar. And then, you may check the file " README. Structural Alphabet Sequence Database (SADB). According to the k. With Structural alphabet sequences.
3d-blast.life.nctu.edu.tw
3D-BLAST Protein Structure Search
http://3d-blast.life.nctu.edu.tw/dbsas-upload.php
Uploading, Please wait . Fri, 19 Aug 2016 03:12:22 0800. 3D-BLAST Protein Structure Search. Input a protein structure as a query to discover its homologous proteins and evolutionary classifications. To obtain more information on that specific field. The standalone 3D-BLAST program. Is avaliable now. Please see Download page. Upload a file in PDB format. Click here. To download an example pdb file. SCOP 1.75 (all). SCOP 1.75 (95%). SCOP 1.75 (40%). Maximum number of hit structures.
3d-blast.life.nctu.edu.tw
3D-BLAST Introduction
http://3d-blast.life.nctu.edu.tw/intro.php
Value calculating from the substitution scoring matrix of structural alphabets. With regard to sensitivity and selectivity of the structural matches, 3D-BLAST compares well to the related programs, although it is by far faster. Our method search more than 10000 protein structures in 1.3 seconds and achieved a good agreement with the results of detailed structure alignment methods. By using kappa ( k. And alpha ( a. Angle (Figure B) defined as in the DSSP program. According to the k. We then enhanced the ...
3d-blast.life.nctu.edu.tw
3D-BLAST (Kappa, Alpha) map
http://3d-blast.life.nctu.edu.tw/kamap.php
A structure fragment (five residues long) is defined by the ( k. Pair angles as shown in Figure A. The k. Angle, ranging from 0 to 180 , of a residue i. Is defined as a bond angle formed by three C. Atoms of residues i. Angle, ranging from -180 to 180 , of a residue i. Is a dihedral angle formed by the four C. Atoms of residues i. Figure A. The definitions of the kappa ( k. And alpha ( a. Map, is able to represent a protein structure. Therefore, each protein structure may form a specific ( k. Angle range...
3d-blast.life.nctu.edu.tw
3D-BLAST Structural alphabet
http://3d-blast.life.nctu.edu.tw/sa.php
The goal of defining a structural alphabet is to code a 3D structure fragment of protein backbones and is to represent a 3D protein structure by a serial of structural alphabets. An alphabet represents pattern profiles of the backbone fragments (five residues long) derived from the pair database, therefore, a protein structure of L. Residues is described by a structural alphabet sequence of L.
3d-blast.life.nctu.edu.tw
3D-BLAST Help
http://3d-blast.life.nctu.edu.tw/help.php
SCOP identifier (Protein domain). Identifier is specified in seven characters: dPPPPCN where d is the SCOP assigned identifier, PPPP is the Protein Data Bank. PDB) assigned identifier, C is the chain identifier, and N indicates the serial number of domains on this protein chain. A user must input a SCOP code that exists in SCOP 1.73 database. Otherwise he/she needs to upload a three-dimensional protein domain structure with PDB format. PDB identifier and chain (Protein chain). PDB ( Protein Data Bank.
3d-blast.life.nctu.edu.tw
3D-BLAST Protein Structure Search
http://3d-blast.life.nctu.edu.tw/dbsas.php
3D-BLAST Protein Structure Search. Input a protein structure as a query to discover its homologous proteins and evolutionary classifications. To obtain more information on that specific field. The standalone 3D-BLAST program. Is avaliable now. Please see Download page. SCOP 1.75 (all). SCOP 1.75 (95%). SCOP 1.75 (40%). Maximum number of hit structures. Vol 8, pp. R31.1 R31.16, 2007. J-M Yang and C.-H. Tung " Protein structure database search and evolutionary classification. Vol 34, pp. 3646-3659, 2006.
3d-blast.life.nctu.edu.tw
3D-BLAST Visitor tracking
http://3d-blast.life.nctu.edu.tw/tracking.php
Log of 30 days. Log of countries (past 30 days). Log of this year. Log of last year.
3d-blast.life.nctu.edu.tw
3D-BLAST Substitution matrix
http://3d-blast.life.nctu.edu.tw/sm.php
Turn that that allow the peptide backbone to fold back and bear great significance in protein structure and function. This value is 11. In total, most of these segments (95.25%) in W are the b. Structural alphabets substitution matrix (SASM) of 3D-BLAST. The scores are high if similar alphabets are aligned, e.g., helix alphabets (A, Y, B, C, and D) are aligned to helix alphabets. In contrast, the scores are low when helix alphabets are aligned to strand alphabets.
