Use of Bioinformatics Tools in Different Spheres of Life Sciences
2014, Journal of Data Mining in Genomics & Proteomics
https://doi.org/10.4172/2153-0602.1000158Abstract
The pace, by which scientific knowledge is being produced and shared today, was never been so fast in the past. Different areas of science are getting closer to each other to give rise new disciplines. Bioinformatics is one of such newly emerging fields, which makes use of computer, mathematics and statistics in molecular biology to archive, retrieve, and analyse biological data. Although yet at infancy, it has become one of the fastest growing fields, and quickly established itself as an integral component of any biological research activity. It is getting popular due to its ability to analyse huge amount of biological data quickly and cost-effectively. Bioinformatics can assist a biologist to extract valuable information from biological data providing various web-and/or computer-based tools, the majority of which are freely available. The present review gives a comprehensive summary of some of these tools available to a life scientist to analyse biological data. Exclusively this review will focus on those areas of biological research, which can be greatly assisted by such tools like analysing a DNA and protein sequence to identify various features, prediction of 3D structure of protein molecules, to study molecular interactions, and to perform simulations to mimic a biological phenomenon to extract useful information from the biological data.
References (162)
- Mount DW (2004) Sequence and genome analysis. New York: Cold Spring.
- Hesper B, Hogeweg P (1970) Bioinformatica:een werkconcept. Kameleon 1: 28-9.
- Hogeweg P (2011) The roots of bioinformatics in theoretical biology. PLoS Comput Biol 7: e1002021.
- Peitsch MC (1996) ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24: 274-279.
- Dibyajyoti S, Bin ET, Swati P (2013) Bioinformatics: The effects on the cost of drug discovery. Galle Med J 18: 44-50.
- Ouzounis CA, Valencia A (2003) Early bioinformatics: the birth of a discipline--a personal view. Bioinformatics 19: 2176-2190.
- Molatudi M, Molotja N, Pouris A (2009) A bibliometric study of bioinformatics research in South Africa. Scientometrics 81: 47-59.
- Ouzounis CA (2012) Rise and demise of bioinformatics? Promise and progress. PLoS Comput Biol 8: e1002487.
- Geer RC, Sayers EW (2003) Entrez: making use of its power. Brief Bioinform 4: 179-184.
- Parmigiani G, Garrett ES, Irizarry RA, Zeger SL (2003) The analysis of gene expression data: an overview of methods and software, Springer, New York.
- Hoersch S, Leroy C, Brown NP, Andrade MA, Sander C (2000) The GeneQuiz web server: protein functional analysis through the Web. Trends Biochem Sci 25: 33-35.
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
- Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
- Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor. Bioinformatics 20: 426-427.
- Thomas P, Starlinger J, Vowinkel A, Arzt S, Leser U (2012) GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res 40: W585-591.
- Page RD (2001) TreeView. Glasgow University, Glasgow, UK.
- Zhang Y, Phillips CA, Rogers GL, Baker EJ, Chesler EJ, et al. (2014) On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types. BMC Bioinformatics 15: 110.
- Stoilov I, Akarsu AN, Alozie I, Child A, Barsoum-Homsy M, et al. (1998) Sequence analysis and homology modeling suggest that primary congenital glaucoma on 2p21 results from mutations disrupting either the hinge region or the conserved core structures of cytochrome P4501B1. Am J Hum Genet 62: 573-584.
- Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, et al. (1999) Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber Lung Dis 79: 329-342.
- Mehmood MA, Xiao X, Hafeez FY, Gai Y, Wang F (2011) Molecular characterization of the modular chitin binding protein Cbp50 from Bacillus thuringiensis serovar konkukian. Antonie Van Leeuwenhoek 100: 445-453.
- Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, et al. (2013) Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. Bioinformation 9: 901-907.
- Kingsford CL, Ayanbule K, Salzberg SL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8: R22.
- Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522.
- Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, et al. (2013) Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder. Nat Commun 4: 2739.
- Peng Z, Lu Y, Li L, Zhao Q, Feng Q, et al. (2013) The draft genome of the fast- growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45: 456-461, 461e1-2.
- Khan FA, Phillips CD, Baker RJ (2014) Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements. Syst Biol 63: 96-110.
- Freckleton RP, Harvey PH, Pagel M (2002) Phylogenetic analysis and comparative data: a test and review of evidence. Am Nat 160: 712-726.
- Price MN, Dehal PS, Arkin AP (2010) FastTree 2--approximately maximum- likelihood trees for large alignments. PLoS One 5: e9490. Volume 5 • Issue 2 • 1000158
- J Data Mining Genomics Proteomics ISSN: 2153-0602 JDMGP, an open access journal
- Bast F (2013) Sequence similarity search, multiple sequence alignment, model selection, distance matrix and phylogeny reconstruction. Nat Protoc.
- Ahmad N, Michoux F, Nixon PJ (2012) Investigating the production of foreign membrane proteins in tobacco chloroplasts: expression of an algal plastid terminal oxidase. PLoS One 7: e41722.
- Chen Y, Wang F, Xu J, Mehmood MA, Xiao X (2011) Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J 5: 843-855.
- Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-370.
- UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42: D191-198.
- Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, et al. (2003) The Protein Information Resource. Nucleic Acids Res 31: 345-347.
- Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank. Nucleic Acids Res 36: D25-30.
- Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, et al. (2005) The EMBL Nucleotide Sequence Database. Nucleic Acids Res 33: D29-33.
- Miyazaki S, Sugawara H, Gojobori T, Tateno Y (2003) DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res 31: 13-16.
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
- Finn RD, Bateman A, Clements J, Marco Punta, Penny C Coggill, et al. (2014) Pfam: the protein families database. Nucl Acids Res 42: D222-D230.
- Gonzalez S, Binato R, Guida L, Mencalha AL, Abdelhay E4 (2014) Conserved transcription factor binding sites suggest an activator basal promoter and a distal inhibitor in the galanin gene promoter in mouse ES cells. Gene 538: 228- 234.
- Fox NK, Brenner SE, Chandonia JM (2014) SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res 42: D304-309.
- Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res 33: D247-251.
- Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, et al. (2013) New and continuing developments at PROSITE. Nucleic Acids Res 41: D344-347.
- Huang JY, Brutlag DL (2001) The EMOTIF database. Nucleic Acids Res 29: 202-204.
- UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36: D190-195.
- Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, et al. (2012) Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40: D453-460.
- Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, et al. (2012) GenBank. Nucleic Acids Res 40: D48-53.
- Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, et al. (2010) Xenbase: gene expression and improved integration. Nucleic Acids Res 38: D607-612.
- St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium (2014) FlyBase 102--advanced approaches to interrogating FlyBase. Nucleic Acids Res 42: D780-788.
- Chou KC, Elrod DW (1999) Protein subcellular location prediction. Protein Eng 12: 107-118.
- Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, et al. (2000) The protein information resource (PIR). Nucleic Acids Res 28: 41-44.
- UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142-148.
- Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35: D301-303.
- Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, et al. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41: D226-232.
- Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, et al. (2014) The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42: D358-363.
- Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, et al. (2002) MINT: a Molecular INTeraction database. FEBS Lett 513: 135-140.
- Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33: D428-432.
- Saier MH Jr, Tran CV, Barabote RD (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 34: D181-186.
- Saier MH Jr, Reddy VS, Tamang DG, Västermark A (2014) The transporter classification database. Nucleic Acids Res 42: D251-258.
- Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42: D490-495.
- Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, et al. (2011) Bioinformatics and systems biology of the lipidome. Chem Rev 111: 6452-6490.
- Huang T, He ZS, Cui WR, Cai YD, Shi XH, et al. (2013) A sequence-based approach for predicting protein disordered regions. Protein Pept Lett 20: 243- 248.
- Zakeri P, Jeuris B, Vandebril R, Moreau Y (2014) Protein fold recognition using geometric kernel data fusion. Bioinformatics 30: 1850-1857.
- Yao L, Evans JA, Rzhetsky A (2010) Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol 28: 161-170.
- Sutcliffe MJ, Haneef I, Carney D, Blundell TL (1987) Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1: 377-384.
- Bates PA, Sternberg MJ (1999) Model building by comparison at CASP3: using expert knowledge and computer automation. Proteins Suppl 3: 47-54.
- Sali A, Blundell T (1994) Comparative protein modelling by satisfaction of spatial restraints. Protein Struc Dist Anal 64: 86.
- Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, et al. (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31: 3784-3788.
- Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725-738.
- Eswar N, Webb B, Martin-Renom MA, Shen MY, Pieper U, et al. (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics.
- Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31: 455-461.
- Sehar U, Mehmood MA, Nawaz S, Nadeem S, Hussain K, et al. (2013) Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis. Bioinformation 9: 725- 729.
- Butt AM, Batool M, Tong Y (2011) Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237. Bioinformation 7: 299-303.
- Ali M, Mehmood MA, Hussain K (2013) Functional annotation of the cda1 gene from Bacillus thuringiensis through homology modeling and molecular docking. Pak J Life Soc Sci 11:190-195.
- Wang L, Huang C, Yang MQ, Yang JY (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol 4 Suppl 1: S3.
- Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, et al. (2014) Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods 11: 94-99.
- Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364.
- Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, et al. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
- Hosur R, Xu J, Bienkowska J, Berger B (2011) iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. J Mol Biol 405: 1295-1310.
- Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, et al. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490: 556-560.
- Valente GT, Acencio ML, Martins C, Lemke N (2013) The development of a universal in silico predictor of protein-protein interactions. PLoS One 8: e65587.
- Zhang Z, Li Y, Lin B, Schroeder M, Huang B (2011) Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 27: 2083-2088.
- de Vries SJ, van Dijk M, Bonvin AM (2010) The HADDOCK web server for data- driven biomolecular docking. Nat Protoc 5: 883-897.
- Plewczynski D, Łaźniewski M, Augustyniak R, Ginalski K (2011) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem 32: 742-755.
- Singh R, Xu J, Berger B (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci U S A 105: 12763-12768.
- Liao CS, Lu K, Baym M, Singh R, Berger B (2009) IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25: i253-258.
- Khan M, Masoud MS, Qasim M, Khan MA, Zubair M, et al. (2013) Molecular screening of phytochemicals from Amelanchier Alnifolia against HCV NS3 protease/helicase using computational docking techniques. Bioinformation 9: 978-982.
- Klingström T, Plewczynski D (2011) Protein-protein interaction and pathway databases, a graphical review. Brief Bioinform 12: 702-713.
- Bader GD, Betel D, Hogue CW (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250.
- Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40: D857-861.
- Cordeiro MN, Speck-Planche A (2012) Computer-aided drug design, synthesis and evaluation of new anti-cancer drugs. Curr Top Med Chem 12: 2703-2704.
- Katara P (2013) Role of bioinformatics and pharmacogenomics in drug discovery and development process. Network Modeling Analysis in Health Informatics and Bioinformatics 2: 225-30.
- Yamanishi Y, Kotera M, Kanehisa M, Goto S (2010) Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 26: i246-254.
- Boruah L, Das A, Nainwal LM, Agarwal N, Shankar B (2013) In-Silico Drug Design: A revolutionary approach to change the concept of current Drug Discovery Process. Ind J Pharm Biologi Res 1: 60-73.
- Lee HM, Giguere PM, Roth BL (2014) DREADDs: novel tools for drug discovery and development. Drug Discov Today 19: 469-473.
- Wishart DS (2005) Bioinformatics in drug development and assessment. Drug Metab Rev 37: 279-310.
- Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3: 935-949.
- Reddy RN, Mutyala R, Aparoy P, Reddanna P, Reddy MR (2007) Computer aided drug design approaches to develop cyclooxygenase based novel anti- inflammatory and anti-cancer drugs. Curr Pharm Des 13: 3505-3517.
- Jayakanthan M, Wadhwa G, Mohan TM, Ponnusamy B, Durai S, et al. (2009) Computer-aided drug design for cancer-causing H-Ras p21 mutant protein. Lett Drug Des Discov 6: 14-20.
- Kim J, Gao L, Tan K (2012) Multi-analyte network markers for tumor prognosis. PLoS One 7: e52973.
- Wu CC, D'Argenio D, Asgharzadeh S, Triche T (2012) TARGETgene: a tool for identification of potential therapeutic targets in cancer. PLoS One 7: e43305.
- Berg EL (2014) Systems biology in drug discovery and development. Drug Discov Today 19: 113-125.
- McDermott JE, Diamond DL, Corley C, Rasmussen AL, Katze MG, et al. (2012) Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis. BMC Syst Biol 6: 28.
- Makhmoudova A, Williams D, Brewer D, Massey S, Patterson J, et al. (2014) Identification of multiple phosphorylation sites on maize endosperm starch branching enzyme IIb, a key enzyme in amylopectin biosynthesis. J Biol Chem 289: 9233-9246.
- Hub JS, de Groot BL (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A 105: 1198-1203.
- Kannan S, Zacharias M (2014) Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations. PLoS One 9: e88383.
- Isin B, Estiu G, Wiest O, Oltvai ZN (2012) Identifying ligand binding conformations of the β2-adrenergic receptor by using its agonists as computational probes. PLoS One 7: e50186.
- Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R (2013) Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 138: 333-408.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
- Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-37.
- Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
- Ganesan N, Bennett NF, Velauthapillai M, Pattabiraman N, Squier R, et al. (2005) Web-based interface facilitating sequence-to-structure analysis of BLAST alignment reports. Biotechniques 39: 186, 188.
- Gasteiger E, Hoogland C, Gattiker A, Ron D Appel, Amos Bairoch, et al. (2005) In: The proteomics protocols handbook; Protein identification and analysis tools on the ExPASy server. Springer 571-607.
- Allen JE, Salzberg SL (2005) JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21: 3596-3603.
- Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts M, et al. (2005) novoSNP, a novel computational tool for sequence variation discovery. Genome Res 15: 436-442.
- Münch R, Hiller K, Grote A, Scheer M, Klein J, et al. (2005) Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21: 4187-4189.
- Unniraman S, Prakash R, Nagaraja V (2002) Conserved economics of transcription termination in eubacteria. Nucleic Acids Res 30: 675-684.
- Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
- Kumar S, Tamura K, Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci 10: 189-191.
- Adachi J, Hasegawa M (1992) MOLPHY, programs for molecular phylogenetics I: PROTML, maximum likelihood inference of protein phylogeny. Institute of Statistical Mathematics, Tokyo.
- Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
- Felsenstein J (1993) PHYLIP phylogeny inference package. Department of Genetics, University of Washington, Seattle.
- Boc A, Diallo AB, Makarenkov V (2012) T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res 40: W573-579.
- Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
- Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191. Volume 5 • Issue 2 • 1000158
- J Data Mining Genomics Proteomics ISSN: 2153-0602 JDMGP, an open access journal
- Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, et al. (2011) The European Nucleotide Archive. Nucleic Acids Res 39: D28-31.
- Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: W116-120.
- Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, et al. (2005) PRIDE: the proteomics identifications database. Proteomics 5: 3537-3545.
- Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-90.
- Rajoka MI, Idrees S, Khalid S, Ehsan B (2014) Medherb: An Interactive Bioinformatics Database and Analysis Resource for Medicinally Important Herbs. Curr Bioinform 9: 23-27.
- Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37: D619-622.
- Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, et al. (2011) dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. Nucleic Acids Res 39: D620-624.
- Kanehisa M (2002) The KEGG database. Silico Simulation of Biological Processes 247: 91-103.
- Yang K, Dinasarapu AR, Reis ES, Deangelis RA, Ricklin D, et al. (2013) CMAP: Complement Map Database. Bioinformatics 29: 1832-1833.
- Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S (2011) Signaling gateway molecule pages--a data model perspective. Bioinformatics 27: 1736-1738.
- Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res 37: D674-679.
- Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, et al. (2007) HMDB: the Human Metabolome Database. Nucleic Acids Res 35: D521-526.
- Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41: D490-498.
- Källberg M, Wang H, Wang S, Peng J, Wang Z, et al. (2012) Template-based protein structure modeling using the RaptorX web server. Nat Protoc 7: 1511- 1522.
- Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ (1998) JPred: a consensus secondary structure prediction server. Bioinformatics 14: 892-893.
- Rost B, Sander C, Schneider R (1994) PHD--an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 10: 53-60.
- Bystroff C, Thorsson V, Baker D (2000) HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 301: 173-190.
- Raghava G (2002) APSSP2: A combination method for protein secondary structure prediction based on neural network and example based learning. CASP5 A-132.
- Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363-371.
- Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40: D302-305.
- Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, et al. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30: 2785-2791.
- Environment MO (2009) Chemical Computing Group. Montreal, Canada.
- Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41: D808-815.
- Di Lena P, Wu G, Martelli PL, Casadio R, Nardini C (2013) MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinformatics 14: 159.
- Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S (2006) Graemlin: general and robust alignment of multiple large interaction networks. Genome Res 16: 1169-1181.
- Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, et al. (2004) PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res 32: W83-88.
- Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T (2006) CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
- Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
- Gao Z, Li H, Zhang H, Liu X, Kang L, et al. (2008) PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics 9: 104.
- Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, et al. (2014) DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 42: D1091-1097.
- Chen X, Ji ZL, Chen YZ (2002) TTD: Therapeutic Target Database. Nucleic Acids Res 30: 412-415.
- Magariños MP1, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, et al. (2012) TDR Targets: a chemogenomics resource for neglected diseases. Nucleic Acids Res 40: D1118-1127.
- Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, et al. (2008) SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res 36: D919-922.
- Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, et al. (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40: D1100-1107.
- Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.