3D-Match and 3D-MatchDB FAST Structural alignment on line

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

[Only registered users see links. ]

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 DIELTQSPPSLPVSLGDQVSISCRSSQSLVSNNRRNYLHWYLQKPGQSPK LVIYKVSNRF
REMARK 1
REMARK 1 58 AGVPSRFSGSGSGTDYTFTISSLQPEDIATYYCQQYQSLPYTFGQGTKLQ IT
REMARK 1 61 SGVPDRFSGSGSGTDFTLKISRVAAEDLGLYFCSQSSHVPLTFGSGTKLE IK
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 KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY VPRNLLGLY
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