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[Computational-biology] New 3D-Match and 3D-MatchDB FAST Structural alignment on line

Nick Grishin grishin at chop.swmed.edu
Tue Mar 21 14:10:02 EST 2006


Webmaster at softberry:
Thanks for the info. How can we download the soft?
Nick



On Mon, 20 Mar 2006 webmaster at softberry.com wrote:

>    3D-Match: Alignment 3D structures of two proteins and
>    3D-MatchDB: - FAST on-line search of nonredundant PDB for structural
> homology with a query protein.
>
> The new programs are available for public use at
>
>  http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=propt
>
> Comparison of 500 structural alignments produced by CE and 3D-Match reveals
> that
> average RMSD of results produced by CE is by 0.13 angstrom lower,
> but alignments by 3D-Match are on average 5.03 residues longer.
>
> It takes 3DMatchDB just  a few minutes to search nonredundant PDB database
> (12,834 proteins with less than 98% sequence similarity) for structural
> homologs
> with a given 3D structure.
>   To increase speed, 3DmatchDB uses an algorithm of fast alignment of
> secondary structure elements (helix, beta-sheet) and a preprocessed PDB
> database that
> has protein secondary structure elements mapped to 3D structures.
> 3DMatchDB performs pairwise structural alignment of a query protein with
> each database entry, and calculates RMSD and Zscore for each pair.
>
> An example of 3DMATCH output:
> ===================================
>
> HEADER    PROTEIN STRUCTURE ALIGNMENT
> COMPND    (A) 1BWW chain A (B) 2BFV chain L
> REMARK   1
> REMARK   1 RMSD on Ca-atoms :  0.817 angstrom
> REMARK   1 Zscore           :  6.230
> REMARK   1 Aligned positions:    107
> REMARK   1 Gap positions    :      5
> REMARK   1 Sequence identity:   54.5 (%)
> REMARK   1
> REMARK   1 Structure based sequence alignment
> REMARK   1
> REMARK   1 3     DIQMTQSPSSLSASVGDRVTITCQASQDII-----KYLNWYQQKPGKAPKLLIYEASNLQ
> REMARK   1 1     DIELTQSPPSLPVSLGDQVSISCRSSQSLVSNNRRNYLHWYLQKPGQSPKLVIYKVSNRF
> REMARK   1
> REMARK   1 58    AGVPSRFSGSGSGTDYTFTISSLQPEDIATYYCQQYQSLPYTFGQGTKLQIT
> REMARK   1 61    SGVPDRFSGSGSGTDFTLKISRVAAEDLGLYFCSQSSHVPLTFGSGTKLEIK
> REMARK   1
> ATOM      1  N   THR A   1     -19.249   5.700 -17.692  1.00 67.85           N
> ATOM      2  CA  THR A   1     -18.745   6.056 -16.364  1.00 64.75           C
> ATOM      3  C   THR A   1     -17.224   6.135 -16.364  1.00 48.48           C
> ATOM      4  O   THR A   1     -16.538   5.185 -16.770  1.00 47.02           O
> ATOM      5  CB  THR A   1     -19.208   5.088 -15.261  1.00 72.33           C
> ATOM      6  OG1 THR A   1     -20.156   4.118 -15.725  1.00 76.14           O
>
>
>
> An example of 3DMATCH-DB output:
> ===================================
>  STRUCTURE DATABASE SEARCHING.
>
>  ID ZScore RMSD Aligned Size Gaps Name
>  1SEM:A 5.7 0.00 9 11 0 MOLECULE: SEM-5; DOMAIN: C-TERMINAL SH3, RESIDUES 155-
> 214; CHAIN: A, B;
>  1QKW:A 5.3 0.63 9 11 0 MOL_ID: 1; MOLECULE: ALPHA II SPECTRIN; CHAIN: A;
> FRAGMENT: SH3 DOMAIN;
>  1QKX:A 5.3 0.62 9 11 0 MOL_ID: 1; MOLECULE: SPECTRIN ALPHA CHAIN; CHAIN: A;
> FRAGMENT: SH3 DOMAIN
>  1NG2:A 5.3 0.65 9 25 0 MOL_ID: 1; MOLECULE: NEUTROPHIL CYTOSOLIC FACTOR 1;
> CHAIN: A; FRAGMENT:
>  1K76:A 5.3 0.59 9 11 0 MOL_ID: 1; MOLECULE: SEX MUSCLE ABNORMAL PROTEIN 5;
> CHAIN: A; FRAGMENT:
>  1GCQ:A 5.2 0.77 9 11 0 MOL_ID: 1; MOLECULE: GROWTH FACTOR RECEPTOR-BOUND
> PROTEIN 2; CHAIN: A, B;
>  1HD3:A 5.2 0.83 9 11 0 MOL_ID: 1; MOLECULE: SPECTRIN ALPHA CHAIN; CHAIN: A;
> FRAGMENT: SH3-DOMAIN
>  1QCF:A 5.2 0.81 9 69 0 MOL_ID: 1; MOLECULE: HAEMATOPOETIC CELL KINASE (HCK);
> CHAIN: A; FRAGMENT:
>  1UUE:A 5.2 0.81 9 11 0 MOL_ID: 1; MOLECULE: SPECTRIN ALPHA CHAIN; SYNONYM:
> SPECTRIN NON-
>  1E6H:A 5.2 0.70 9 11 0 MOL_ID: 1; MOLECULE: SPECTRIN ALPHA CHAIN; CHAIN: A;
> FRAGMENT: SH3-DOMAIN
>  1JO8:A 5.0 1.01 9 11 0 MOL_ID: 1; MOLECULE: ACTIN BINDING PROTEIN; CHAIN: A;
> FRAGMENT: SH3
>  1JEG:A 5.0 1.01 9 11 0 MOL_ID: 1; MOLECULE: TYROSINE-PROTEIN KINASE CSK;
> CHAIN: A; FRAGMENT: SH3
>  1E6G:A 5.0 0.93 9 11 0 MOL_ID: 1; MOLECULE: SPECTRIN ALPHA CHAIN; CHAIN: A;
> FRAGMENT: SH3-DOMAIN
>  1SHF:A 5.0 1.02 9 11 0 FYN PROTO-ONCOGENE TYROSINE KINASE (E.C.2.7.1.112)
> (SH3 DOMAIN)
>  1EFN:A 4.9 1.21 9 11 0 MOL_ID: 1; MOLECULE: FYN TYROSINE KINASE; CHAIN: A, C;
> FRAGMENT: SH3
>  1UGV:A 4.7 1.41 9 11 0 MOL_ID: 1; MOLECULE: OLYGOPHRENIN-1 LIKE PROTEIN;
> CHAIN: A; FRAGMENT: SH3
>  1BBZ:A 4.7 1.41 9 11 0 MOL_ID: 1; MOLECULE: ABL TYROSINE KINASE; CHAIN: A, C,
> E, G; FRAGMENT:
>  1YCS:B 4.7 1.26 9 28 0 MOL_ID: 1; MOLECULE: P53; CHAIN: A; FRAGMENT: RESIDUES
> 97 - 287;
>  1GL5:A 4.7 1.32 9 10 0 MOL_ID: 1; MOLECULE: TYROSINE-PROTEIN KINASE TEC;
> CHAIN: A; FRAGMENT: SH3
>  1UJ0:A 4.7 1.37 9 10 0 MOL_ID: 1; MOLECULE: SIGNAL TRANSDUCING ADAPTOR
> MOLECULE (SH3 DOMAIN AND
>  1BBZ:E 4.6 1.45 9 11 0 MOL_ID: 1; MOLECULE: ABL TYROSINE KINASE; CHAIN: A, C,
> E, G; FRAGMENT:
>  1H92:A 4.4 0.81 6 11 0 MOL_ID: 1; MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN
> KINASE LCK; CHAIN:
> ......................................................
>
> For each found homolo, a structural alignment can be output:
>
> PROTEIN STRUCTURE ALIGNMENT.
>
> HEADER    PROTEIN STRUCTURE ALIGNMENT
> COMPND    (A) 1SEM chain A (B) 1YCS chain B
> REMARK   1
> REMARK   1 RMSD on Ca-atoms:  1.084 angstrom
> REMARK   1 Zscore          :  4.890
> REMARK   1
> REMARK   1
> REMARK   1 Alignment
> REMARK   1
> REMARK   1 156   TKFVQALFDFNPQESGELAFKRGDVITLINKD---DPNWWEGQLNNRRGIFPSNYVCPY
> REMARK   1 460   KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGYVPRNLLGLY
> REMARK   1
> ATOM      1  N   GLU A 155      10.819  -4.205  14.117  1.00 57.62      1SEM
> 139
> ATOM      2  CA  GLU A 155       9.614  -5.059  13.924  1.00 55.34      1SEM
> 140
> ATOM      3  C   GLU A 155       9.081  -4.788  12.519  1.00 49.05      1SEM
> 141
> ATOM      4  O   GLU A 155       9.313  -3.718  11.961  1.00 49.97      1SEM
> 142
>
>
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