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Structural and Functional Bioinformatics Letters in Health and Biological Sciences ISSN:2475-6245 Research Article OPEN ACCESS Structural and Functional Bioinformatics Nida Tabassum Khan* Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology Engineering and Management Sciences,(BUITEMS),Quetta, Pakistan *Corresponding author: Nida Tabassum Khan, Department of Biotechnology, Faculty of Life Sciences and Informatics, Baloch- istan University of Information Technology Engineering and Management Sciences, (BUITEMS), Quetta, Pakistan, Tel: 03368164903; E-mail: [email protected] Received date: January 26, 2018 Accepted date: February 22, 2018 Published date: February 26, 2018 Citation: Khan, N.T. Structural and Functional Bioinformatics. (2018) Lett Health Biol Sci 3(1): 7- 11. Abstract: Structural and functional bioinformatics help us to design and formulate prognostic computational models and frameworks that exploit our growing knowledge of biological macromolecules in terms of their structural orga- nization and functional capabilities. Integration of structural and functional biochemistry of macromolecules with informatics empowers significant progress in understanding the fundamentals of biology. Keywords: Cath; Scop; Haddock; Prosite; Vanted; Brenda Introduction Structural and functional bioinformatics aimed to unravel biological problems by analyzing sequences of biological mol- ecules such as DNA and protein using computational algorithms, informatics tools and software’s to assess molecular data[1]. Some of the applications of this novel field are given below: Prediction of protein structure: Understanding the correlation between amino acid sequence and the three dimensional structure of protein, it can be helpful for determining protein structure from its amino acid sequence[2]. Numerous bioinformatics tools could be utilized for protein structure and function prediction including secondary structure prediction[3], homology model- ing[4], protein threading[5], ab initio methods[6], prediction of motif[7], domain[8], transmembrane helix[9], signal peptide[10] etc. Some of these tools and databases used are summarized below in Table 1. Table 1: Protein structure/function prediction software’s and databases. S.no Tools and Databases Purpose 1 PDB (Protein Data Bank) Universal storage of 3D structure data of macromolecules. Providing methods for visu- alizing the structure and downloading structural information[11] 2 MMDB (NCBI Structure Database) Includes database of 3D structure of bimolecules. Provides information on biological functions of proteins, on mechanisms related to their functions and on relationship be- tween biomolecules and their evolutionary history[12] 3 BLAST (Basic Local Alignment Search Tool) Searches for regions of local similarity in a protein or DNA sequence[13] 4 SWISS PDB Viewer Analyze structural alignment of proteins and provide comparison of their active sites, their amino acid mutations angles, distances and H bonds between their atoms[14] 5 PDBsum Consists of images of structure, detailed structural analysis derived from PROMOTIF program, schematic graphs of interactions, summary PROCHEK results etc[15] Copy Rights: © 2018 Khan, N.T. This is an Open access article distributed under the terms of Creative Commons Attribution 4.0 International License. DOI: 10.15436/2475-6245.18.1860 Vol 3:1 pp7 Citation: Khan, N.T. Structural and Functional Bioinformatics. (2018) Lett Health Biol Sci 3(1): 7- 11. 6 Ligplot Determine interaction between proteins, ligands, hydrogen atoms, hydrophobic interac- tions etc[16] 7 SCOP Database containing detailed information of protein structure and phylogenetics[17] 8 CATH (Class, Architecture, Topology and Database that stores hierarchical classification for domain structures of proteins[18] Homologous super family) 9 Composition Profiler Bioinformatics tool for determining amino acids enrichment or depletion based on their physicochemical or structural features[19] 10 Prosite/ Interpro Determines protein families, conserved domains, motifs etc[20] 11 Pfam Determines protein families[21] 12 SWISS PROT Database of annotated protein sequences[22] 13 PRIDE (Proteomics Identifications Database) Contain information on functional characterization and post-translation modification of proteins and peptides[23] 14 SGMP (Signaling Gateway Molecule Pages) Database contains information on functional states of proteins involved in signal trans- duction pathways[24] 15 ProtParam Tool to find proteins physico-chemical properties[25] 18 SMART(Simple Modular Architecture Re- Defines multiple information about the query protein[26] trieval Tool) 19 Auto Dock Determines protein-ligand interaction[27] 20 HADDOCK Determines modeling and bio-molecular[28] 21 BIND Database that provides information on molecular interaction of biological molecules[29] 22 APSSP2 Determines proteins secondary structure[30] 23 MODELLER Determines3D structure of protein[31] 24 Phyre and Phyre2 Find protein structure[32] Few bioinformatics tools and databases for functional analysis of large gene are summarized below in Table 2. Table 2: Tools for structural and functional analysis of gene. S.no Tools and Databases Purpose 1 Gene Ontology Systematically dissect large gene lists[33] 2 Onto-Express, MAP Finder, Go Miner, DAVID, EASE, Gene MergeFun- Analysis of gene-annotation enrichment[34-40] cAssociate etc 3 REPAIRtoire(Examples Repair GENES, Human DNA Repair Genes, Re- Contains data on all DNA repair systems and proteins from pair-Fun Map and GeneSNPs etc) model organisms[41,42] 4 BRENDA (BRaunschweig Enzyme Database) Database contains information on enzymes properties etc[43] 5 Pathway Commons Contains data on biological pathways including macromole- cule interactions, biochemical reactions, complex assembly, transport, catalysis events, etc[44] 6 OriDB (DNA replication), Data base (Replication Domain, apoptosis), Databases contains data on DNA metabolism[45-49] Telomerase database (telomere maintenance), REBASE (DNA restriction and modification), and DAnCER (epigenetic/chromatin modification ) 7 JIGSAW Determine genes, splicing sites etc[50] 8 novoSNP Find point mutation in DNA sequence[51] 9 PPP(Prokaryotic promoter prediction) Tool to determine promoter in a gene[52] 10 WebGeSTer Database to find the termination sites during transcription in the genes[53] 11 Genscan Determine exon-intron sites in sequences[54] Few bioinformatics tools and databases for analysis of lipids are summarized below in Table 3. www.ommegaonline.org Vol 3:1 pp8 Short title: Bioinformatics Table 3: Tools for analysis of lipids. S.no Tools and Databases Purpose 1 magnet Software enables retrieval and visualization of biological relationships across heterogeneous data sources from an integrated database[55] 2 VANTED Enable importing and customization of KEGG lipid-specific pathways[56] 3 GOLD LIPID MAPS Proteome Database (LMPD), LIP- Database of genomics of lipid-associated disorders[57-60] ID BANK, LIPIDAT and LMSD Conclusion Data Bank, 1999–. (2006) In International Tables for Crys- tallography Volume F: Crystallography of biological mac- romolecules: 675-684. Progress in the field of structural and functional bioin- formatics includes future contribution to structural and function- Pubmed | Crossref | Others al understanding of the macromolecules such as DNA, proteins, 12. Chen, J., Anderson, J.B., DeWeese-Scott, C., et al. MMDB: lipids etc for the better apprehension of the biological processes Entrez’s 3D-structure database. (2003)Nucleic Acids Res 31(1): 474-477. and pathways on which the origin of life rely. Pubmed | Crossref | Others References 13. Altschul, S.F., Gish, W., Miller, W., et al. Basic local align- ment search tool. (1990) J Mol Biol 215(3): 403-410. 1. Chou, K.C. Structural bioinformatics and its impact to Pubmed | Crossref | Others biomedical science. (2004) Current medicinal chemistry 14. Kaplan, W., Littlejohn, T.G. Swiss-PDB viewer (deep 11(16): 2105-2134. view). (2001) Brief Bioinform 2(2): 195-197. Pubmed | Crossref | Others Pubmed | Crossref | Others 2. Rokde,C.N., Kshirsagar, M. Bioinformatics: Protein struc- 15. Laskowski, R.A. PDBsum: summaries and analyses of PDB ture prediction.(2013) In Computing, Communications and structures. (2001) Nucleic Acids Res 29(1): 221-222. Networking Technologies (ICCCNT), 2013 Fourth Interna- tional Conference on IEEE: (1-5). Pubmed | Crossref | Others Pubmed | Crossref | Others 16. Wallace, A.C., Laskowski, R.A., Thornton, J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand 3. Barton, G.J. Protein secondary structure prediction. (1995) interactions. (1995) Protein Eng 8(2): 127-134. Current opinion in structural biology 5(3): 372-376. Pubmed | Crossref | Others Pubmed | Crossref | Others 17. Murzin, A.G., Brenner, S.E., Hubbard, T., et al. SCOP: a 4. Bordoli, L., Kiefer, F., Arnold, K., et al. Protein structure structural classification of proteins database for the inves- homology modeling using SWISS-MODEL workspace. tigation of sequences and structures. (1995) J Mol Biol (2009) Nat Protoc 4(1): 1-13. 247(4): 536-540. Pubmed | Crossref | Others Pubmed | Crossref | Others 5. Cristobal, S., Zemla, A., Fischer, D., et al. A study of quality 18. Orengo, C.A., Pearl, F.M., Thornton, J.M.The CATH do- measures for protein threading models. (2001) BMC bioin- main structure database. (2005) Structural Bioinformatics formatics 2(1): 5. 44: 249-271. Pubmed | Crossref | Others Pubmed | Crossref | Others 6. Chivian, D., Robertson,
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