[Protein-analysis] New 3D-Match and 3D-MatchDB FAST Structural alignment on line

[victor at softberry.com]

   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