Superimpose:: a 3D structural superposition server

被引：29

作者：

Bauer, Raphael A. ^{[1
,2
,3
]}

Bourne, Philip E. ^{[4
]}

Formella, Arno ^{[5
]}

Froemmel, Cornelius ^{[6
]}

Gille, Christoph ^{[7
]}

Goede, Andrean ^{[7
]}

Guerler, Aysam ^{[1
,8
]}

Hoppe, Andreas ^{[7
]}

Knapp, Ernst-Walter ^{[8
]}

Poeschel, Thorsten ^{[9
]}

Wittig, Burghardt

Ziegler, Valentin ^{[10
]}

Preissner, Robert ^{[1
,3
]}

机构：

[1] Genom & Syst Biol Mol Networks, Grad Sch, D-10117 Berlin, Germany

[2] Charite Univ Med Berlin, Struct Bioinformat Grp, D-14195 Berlin, Germany

[3] Charite Univ Med Berlin, Inst Mol Biol & Bioinformat, D-14195 Berlin, Germany

[4] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[5] Univ Vigo, Dept Comp Sci, Orense 32004, Spain

[6] Univ Gottingen, Med Univ, D-37075 Gottingen, Germany

[7] Charite, Computat Syst Biochem Grp, D-10117 Berlin, Germany

[8] Free Univ Berlin, Inst Chem & Biochem, D-14195 Berlin, Germany

[9] Univ Bayreuth, Inst Phys, D-95440 Bayreuth, Germany

[10] Humboldt Univ, D-10099 Berlin, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkn285

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Superimpose webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e. g. drugs), parts of large structures (e. g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimpose ' assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimpose ' server is available at: http://bioinformatics.charite.de/superimpose.

引用

页码：W47 / W54

页数：8

共 39 条

[1] Molecular similarity and property similarity [J].

Barbosa, F ;

Horvath, D .

CURRENT TOPICS IN MEDICINAL CHEMISTRY, 2004, 4 (06) :589-600

[2] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[3] The ASTRAL Compendium in 2004 [J].

Chandonia, JM ;

Hon, G ;

Walker, NS ;

Lo Conte, L ;

Koehl, P ;

Levitt, M ;

Brenner, SE .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D189-D192

[4] Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients [J].

Chen, X ;

Reynolds, CH .

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 2002, 42 (06) :1407-1414

[5] Ligand Depot: a data warehouse for ligands bound to macromolecules [J].

Feng, ZK ;

Chen, L ;

Maddula, H ;

Akcan, O ;

Oughtred, R ;

Berman, HM ;

Westbrook, J .

BIOINFORMATICS, 2004, 20 (13) :2153-2155

[6]

FORMELLA A, 2005, P BIOINF KNOWL DISC, P53

[7] Accelerating screening of 3D protein data with a graph theoretical approach [J].

Frömmel, C ;

Gille, C ;

Goede, A ;

Gröpl, C ;

Hougardy, S ;

Nierhoff, T ;

Preissner, R ;

Thimm, M .

BIOINFORMATICS, 2003, 19 (18) :2442-2447

[8] New sequential and parallel derivative-free algorithms for unconstrained minimization [J].

García-Palomares, UM ;

Rodríguez, JF .

SIAM JOURNAL ON OPTIMIZATION, 2002, 13 (01) :79-96

[9] STRAP:: editor for STRuctural Alignments of Proteins [J].

Gille, C ;

Frömmel, C .

BIOINFORMATICS, 2001, 17 (04) :377-378

[10] SUPERFICIAL - Surface mapping of proteins via structure-based peptide library design [J].

Goede, A ;

Jaeger, IS ;

Preissner, R .

BMC BIOINFORMATICS, 2005, 6 (1)

← 1 2 3 4 →