[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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