Analysis of Protein Structure in Silico

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1 49 20 : Analysis of Protein Structure in Silico Michihiro OGAWA* *Department of Microbiology, Kyoto Pharmaceutical University N 20 N 20 N 3 sosuiframe0.html SOSUI Exec 1 FASTA 10 99% 20 α β SOSUI Misasaginakauchi-cho, Yamashina-ku, Kyoto , Japan Fig. 1. Screenshot of SOSUI server of Tokyo University of Agriculture and technology.

2 SCOP CATH Fig. 2. Screenshot of SCOP (Strucutre Classification of Proteins) database. Medical Research Council. RasMol PDB Protein Data Bank 4 osaka-u.ac.jp/pdb/ 3000 PDB ,152 - RPS-BLAST Reverse PSI-BLAST nig.ac.jp/~genome/grpsblt.html SEARCH PSI-BLAST PDB PDB- BLAST PDB Fig. 3. Screenshot of CATH protein structure classification database. University College London. Fig. 4. Screenshot of PDB (Protein Data Bank). Osaka University.

3 51 Fig. 5. Screenshot of RPS-BLAST (Reverse Position- Specific BLAST) server. National Institute of Genetics, Japan. Fig. 6. Screenshot of 3D-PSSM (3-dimentional position-specific scoring matrix) fold recognition server. Imperical College London. CASP6 Critical Assessment of Techniques for Protein Structure Prediction; Casp6.html FORTE 12 FAMS 6 ac.jp/fams/ 3D-PSSM 2 mgenthreader psipred/ 3D-PSSM 1D 3D mgenthreader GenTHREADER 7 3D-PSSM Phyre Fig. 7. Screenshot of PSIPRED protein structure prediction server. University College London. CASP6 Ginalski

4 Fig. 8. Screenshot of BioInfoBank meta server for prediction of protein structure and function. BioInfoBank Institute, Poland. Fig. 9. Screenshot of RasMol, the viewer of macromolecular structure. 1 Galinski 8 3D-SHOTGUN 4 Pcons DS Modeling Accelrys MOE RasMol index2.htm Windows MacOS rasmol_manual/rasmol/rasmol.html ProteinExplorer: Chime: edu/microbio/chime/ 1 Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ Gapped BLAST and PSI- BLAST : A new generation of protein database search programs. Nucl Acids Res 25 : Bates PA, Kelley LA, MacCallum RM, Sternberg MJ Enhancement of protein modelling by human intervention in applying the automatic programs 3D-JIGSAW and 3D- PSSM. Proteins 45(Suppl 5) : Chothia C, Lesk AM The relation between the divergence of sequence and structure in proteins. EMBO J 5 : Fischer D D-SHOTGUN : A novel, cooperative, fold-recognition meta-predictor. Proteins 51 : Hirokawa T, Sear BC, Mitaku S SOSUI : Classification and secondary structure prediction system for membrane proteins. Bioinformatics 14 : Iwadate M, Ebisawa K, Umeyama H Comparative Modeling of CAFASP2 Competition. Chem-Bio Informatics J 1 : Jones DT GenTHREADER : an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287 : McGuffin LJ, Bryson K, Jones DT The PSIPRED protein structure prediction server. Bioinformatics 16 :

5 53 9 Murzin AG, Brenner SE, Hubbard T, Chothia C SCOP : a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247 : : Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucl Acids Res 33 : D248 D Tomii K, Akiyama Y FORTE : a profile-profile comparison tool for protein fold recognition. Bioinformatics 20 : Wallner B, Elofsson A Pcons5 : Combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21 :

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