* Corresponding authors

CURRENT SCIENCE, VOL. 92, NO. 1, 10 JANUARY 2007 29 The team consists of Tata Consultancy Services: M. Vidyasagar, S. Mande, S. Rajgopal, B. Gopalkrishnan, S. T. P. T. Srinivas, C. Uma Maheswara Rao, T. Kathiravan, K. Mastanarao, S. Narendranath, S. Rohini, A. Irshad, T. Murali, C. Subrahmanyam, T. Mona, S. Sankha, V. Priya, D. Suman, V. V. Raja Rao, P. Nageswara Rao, R. Issaac, H. Yashodeep, B. Arundhoti, G. Nishant, S Jignesh, K. S. Chaitanya, S. P. V. Prasad Reddy; Bose Institute: P. Chakraborty; Centre for DNA Fingerprinting and Diagnosis: S. E. Hasnain, S. Mande, A. Nagarajaram, A. Ranjan, M. S. Acharya, M. Anwaruddin, S. K. Arun, Gyanrajkumar, D. Kumar, S. Priya, S. Ranjan, B. R. Reddi, J. Seshadri, P. Sravan Kumar, S. Swaminathan, P. Umadevi, V. Vindal, S. Vijaykrishnan; Central Drug Research Institute: A. K. Saxena, A. Dixit, P. Prathipati, S. K. Kashaw; Indian Institute of Chemical Biology: C. Mandal, S. Bag; Indian Institute of Science: N. Balakrishnan, M. Bansal, N. R. Chandra*, M. R. N. Murthy, S. Ramakumar, K. Sekar, N. Srinivasan, K. Suguna, S. Vishveshwara*, R. Anandhi, Bhadra, S. Das, P. Hansia, S. Hariharaputran, J. Jeyakani, R. Karthikeyan, R. K. Pandey, C. S. Swamy, B. Vasanthakumar; Indian Institute of Technology Bombay: P. V. Balaji, R. Y. Patel; Indian Institute of Technology Delhi: B. Jayaram, S. A. Shaikh; Indian Institute of Technology Kharagpur: P. P. Chakrabarti, A. Banerjee, A. Chakrabarti; Indian Statistical Institute: R. L. Karandikar, Delhi and P. Chaudhuri, Kolkata; Institute of Microbial Technology: G. P. S. Raghava, A. Ghosh; Institute of Bioinformatics and Applied Biotechnology: M. Bansal, N. Paramsivam; Institute of Genomics and Integrative Biology: S. K. Brahmachari, D. Dash, C. Balasubramaniam, A. Basu, P. Biswas, M. Hariharan, R. Mathur, K. S. Sandhu, V. Scaria, R. Shankar; International Institute of Information Technology: P. J. Narayanan, V. Jain, Nirnimesh; Madurai Kamaraj University: S. Krishnaswamy, V. Alaguraj, R. Marikkannu, A. V. S. K. Mohan Katta, N. Krishnan, K. V. Srividhya, P. J. Eswari; National Institute of Pharmaceutical Education and Research: P. V. Bharatam, P. Iqbal; Saha Institute of Nuclear Physics: D. Bhattacharyya; University of Hyderabad: G. R. Desiraju, J. J. Kumar, M. Ravikumar; University of Madras: M. Gautham, P. A. Prasad and D. Bharanidharan. *For correspondence. (nchandra@physics.iisc.ernet.in; sv@mbu.iisc.ernet.in) BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration)

Sarita Ranjan | Jayashree Seshadri | Vaibhav Vindal | Dhiraj Kumar | P. J. Narayanan | T. Murali | Analabha Basu | Gautam R. Desiraju | S. Narendranath | Narayanaswamy Balakrishnan | M. Vidyasagar | C. S. Swamy | Pansy Iqbal | Dhananjay Bhattacharyya | Gajendra P S Raghava | R. Karthikeyan | Debasis Dash | Vinod Scaria | C. Mandal | Prasad V. Bharatam | Arup Ghosh | P. Umadevi | V. R. Rao | Sridhar Hariharaputran | A. Chakrabarti | Sumit K. Bag | Petety V. Balaji | Soma Das | A. V. S. K. Mohan Katta | P J Narayanan | Narayanaswamy Srinivasan | S. Rohini | T. Kathiravan | S. A. Shaikh | Philip Prathipati | V. V. Raja Rao | S. Ramakumar | R. L. Karandikar | Shekhar C. Mande | S. Rajgopal | B. Gopalkrishnan | S. T. P. T. Srinivas | C. Uma Maheswara Rao | K. Mastanarao | A. Irshad | C. Subrahmanyam | T. Mona | S. Sankha | V. Priya | D. Suman | P. Nageswara Rao | R. Issaac | H. Yashodeep | B. Arundhoti | G. Nishant | S. Jignesh | K. S. Chaitanya | S. P. V. Prasad Reddy | Pampa Chakraborty | Seyed E. Hasnain | A. Nagarajaram | Akash Ranjan | Moulinath Acharya | M. Anwaruddin | S. K. Arun | Gyanrajkumar | S. Priya | B. R. Reddi | P. Sravan Kumar | Soumya Swaminathan | S. Vijaykrishnan | Anil K. Saxena | A. Dixit | S. K. Kashaw | Manju Bansal | Nagasuma Chandra | Mathur R. N. Murthy | Kanagaraj Sekar | Kaza Suguna | Saraswathi Vishveshwara | R. Anandhi Bhadra | P. Hansia | Justin Jeyakani | R. K. Pandey | B. Vasanthakumar | Ronak Y. Patel | B. Jayaram | Pinak Chakrabarti | A. Banerjee | P. Chaudhuri | N. Paramsivam | Samir K. Brahmachari | C. Balasubramaniam | Parbati Biswas | Manoj Hariharan | R. Mathur | K. S. Sandhu | Ravi Shankar | V. Jain | Sankaran Krishnaswamy | V. Alaguraj | R. Marikkannu | N. Krishnan | K. V. Srividhya | P. J. Eswari | J. J. Kumar | M. Ravikumar | M. Gautham | P. A. Prasad | D. Bharanidharan | NMITLI-BioSuite Team | M. Vidyasagar | R. Karandikar | P. Chaudhuri | P. Narayanan | G. Desiraju | Gajendra P.S. Raghava | M. Bansal | S. Swaminathan | A. Dixit | K. Sandhu | N. Chandra | S. Vishveshwara | P. Hansia | D. Dash | V. Scaria | S. Brahmachari | M. Hariharan | S. Ramakumar | P. Prathipati | N. Srinivasan | A. Chakrabarti | A. Saxena | D. Bhattacharyya | K. Sekar | P. Biswas | S. Shaikh | B. Jayaram | K. Suguna | S. Mande | P. V. Balaji | J. Kumar | Dhiraj Kumar | T. Murali | J. Jeyakani | N. Balakrishnan | R. Shankar | A. Basu | P. Bharatam | S. Kashaw | S. Narendranath | Soma Das | P. Prasad | S. Krishnaswamy | A. Ranjan | C. Mandal | S. Srinivas | S. Hariharaputran | M. Murthy | D. Bharanidharan | A. M. Katta | B. Vasanthakumar | M. Ravikumar | V. Vindal | A. Ghosh | A. Irshad | C. Swamy | Sumit K Bag | S. Rajgopal | M. Gautham | C. Subrahmanyam | P. Iqbal | T. Kathiravan | V. Priya | A. Banerjee | R. Karthikeyan | P. Chakraborty | S. E. Hasnain | Ronak Y. Patel | Moulinath Acharya | K. Srividhya | P. Umadevi | D. Suman | R. Marikkannu | B. Gopalkrishnan | C. U. M. Rao | K. Mastanarao | S. Rohini | T. Mona | S. Sankha | P. N. Rao | R. Issaac | H. Yashodeep | B. Arundhoti | G. Nishant | S. Jignesh | K. Chaitanya | S. Reddy | A. Nagarajaram | M. Anwaruddin | S. K. Arun | S. Priya | Sarita Ranjan | J. Seshadri | P. Kumar | S. Vijaykrishnan | R. Bhadra | R. K. Pandey | P. Chakrabarti | N. Paramsivam | C. Balasubramaniam | R. Mathur | V. Jain | V. Alaguraj | N. Krishnan | NMITLI-BioSuite Team | Marianne-Pepin

[1]  M. G. Rossmann,et al.  International Tables for Crystallography: Crystallography of biological macromolecules , 2006 .

[2]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[3]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[4]  Debasis Dash,et al.  CoPS: Comprehensive Peptide Signature Database , 2004, Bioinform..

[5]  C. Elkan,et al.  Unsupervised learning of multiple motifs in biopolymers using expectation maximization , 1995, Machine Learning.

[6]  Ch. Kiran Kumar,et al.  SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules , 2003, Nucleic Acids Res..

[7]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[8]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[9]  David L Hyndman,et al.  PCR primer design. , 2003, Methods in molecular biology.

[10]  Erik L L Sonnhammer,et al.  Quality assessment of multiple alignment programs , 2002, FEBS letters.

[11]  Pinak Chakrabarti,et al.  Aromatic-aromatic interactions in and around α-helices , 2002 .

[12]  Roberto Todeschini,et al.  Handbook of Molecular Descriptors , 2002 .

[13]  Pinak Chakrabarti,et al.  Aromatic-aromatic interactions in and around alpha-helices. , 2002, Protein engineering.

[14]  S C Basak,et al.  Molecular similarity-based estimation of properties: a comparison of three structure spaces. , 2001, Journal of molecular graphics & modelling.

[15]  Y. Kurogi,et al.  Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. , 2001, Current medicinal chemistry.

[16]  Raja Mazumder,et al.  GeneOrder: comparing the order of genes in small genomes , 2001, Bioinform..

[17]  Anton J. Enright,et al.  GeneRAGE: a robust algorithm for sequence clustering and domain detection , 2000, Bioinform..

[18]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[19]  S H Kim,et al.  Environment-dependent residue contact energies for proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. B. Boyd.  Chemical Applications of Molecular Modelling, Jonathan M. Goodman (Ed.). (University of Cambridge). Royal Society of Chemistry (1998), xv + 216, ISBN: 0-85404-579-1 , 2000 .

[21]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[22]  Osman F. Güner,et al.  Pharmacophore perception, development, and use in drug design , 2000 .

[23]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[24]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[25]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[26]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[27]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .

[28]  S. Salzberg,et al.  Alignment of whole genomes. , 1999, Nucleic acids research.

[29]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[30]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[31]  Durbin,et al.  Biological Sequence Analysis , 1998 .

[32]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[33]  Michael Gribskov,et al.  Combining evidence using p-values: application to sequence homology searches , 1998, Bioinform..

[34]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[35]  Patrick Argos,et al.  Prediction of Membrane Protein Topology Utilizing Multiple Sequence Alignments , 1997, Journal of protein chemistry.

[36]  A Elofsson,et al.  Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. , 1997, Protein engineering.

[37]  P K Ponnuswamy,et al.  Identification of membrane spanning beta strands in bacterial porins. , 1997, Protein engineering.

[38]  Gregory D Schuler,et al.  Sequence mapping by electronic PCR , 1997, Genome research.

[39]  Dan Gusfield,et al.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[40]  V. Brendel,et al.  Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. , 1996, Nucleic acids research.

[41]  D. Hoekman.  Exploring QSAR Fundamentals and Applications in Chemistry and Biology, Volume 1. Hydrophobic, Electronic and Steric Constants, Volume 2 J. Am. Chem. Soc. 1995, 117, 9782 , 1996 .

[42]  Huaiyu Zhu,et al.  No Free Lunch for Cross-Validation , 1996, Neural Computation.

[43]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[44]  Michael Gribskov,et al.  The Megaprior Heuristic for Discovering Protein Sequence Patterns , 1996, ISMB.

[45]  Andrew Smellie,et al.  Identification of Common Functional Configurations Among Molecules , 1996, J. Chem. Inf. Comput. Sci..

[46]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[47]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[48]  W R Taylor,et al.  SSAP: sequential structure alignment program for protein structure comparison. , 1996, Methods in enzymology.

[49]  J. Gibrat,et al.  GOR method for predicting protein secondary structure from amino acid sequence. , 1996, Methods in enzymology.

[50]  Gareth Jones,et al.  A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..

[51]  M. Levitt,et al.  The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. , 1995, Journal of molecular biology.

[52]  B. Ravi,et al.  NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures , 1995, Comput. Appl. Biosci..

[53]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[54]  Chris Sander,et al.  The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies , 1995, J. Comput. Chem..

[55]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[56]  David J. Thuente,et al.  Line search algorithms with guaranteed sufficient decrease , 1994, TOMS.

[57]  J. Thornton,et al.  Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? , 1994, Journal of molecular biology.

[58]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[59]  D. Haussler,et al.  Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.

[60]  Gad M. Landau,et al.  An Algorithm for Approximate Tandem Repeats , 1993, CPM.

[61]  Mark Borodovsky,et al.  GENMARK: Parallel Gene Recognition for Both DNA Strands , 1993, Comput. Chem..

[62]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[63]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[64]  Roland L. Dunbrack,et al.  Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.

[65]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[66]  X. Huang,et al.  A contig assembly program based on sensitive detection of fragment overlaps. , 1992, Genomics.

[67]  K. Tamura,et al.  Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. , 1992, Molecular biology and evolution.

[68]  Andrew C. Good,et al.  Utilization of Gaussian functions for the rapid evaluation of molecular similarity , 1992, J. Chem. Inf. Comput. Sci..

[69]  Rainer Fuchs,et al.  CLUSTAL V: improved software for multiple sequence alignment , 1992, Comput. Appl. Biosci..

[70]  Jorge Nocedal,et al.  Global Convergence Properties of Conjugate Gradient Methods for Optimization , 1992, SIAM J. Optim..

[71]  A. Lupas,et al.  Predicting coiled coils from protein sequences , 1991, Science.

[72]  B. Honig,et al.  A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .

[73]  C. Branden,et al.  Introduction to protein structure , 1991 .

[74]  D. Eisenberg,et al.  A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.

[75]  P. Tongaonkar,et al.  A semi‐empirical method for prediction of antigenic determinants on protein antigens , 1990, FEBS letters.

[76]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[77]  I. Dodd,et al.  Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. , 1990, Nucleic acids research.

[78]  Eugene W. Myers,et al.  Basic local alignment search tool. Journal of Molecular Biology , 1990 .

[79]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[80]  D. Turner,et al.  Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[81]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[82]  B Jayaram,et al.  The electrostatic potential of B‐DNA , 1989, Biopolymers.

[83]  M. Zuker.  On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[84]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[85]  S. Watowich,et al.  A stable, rapidly converging conjugate gradient method for energy minimization , 1988 .

[86]  J. Gibrat,et al.  Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. , 1987, Journal of molecular biology.

[87]  T. Blundell,et al.  Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.

[88]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[89]  J. Hartigan,et al.  Asynchronous distance between homologous DNA sequences. , 1987, Biometrics.

[90]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[91]  Michael L. Connolly,et al.  Computation of molecular volume , 1985 .

[92]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[93]  M. Nei,et al.  Estimation of evolutionary distance between nucleotide sequences. , 1984, Molecular biology and evolution.

[94]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[95]  E. Baker,et al.  Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.

[96]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[97]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[98]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[99]  O. Gotoh.  An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[100]  David Eisenberg,et al.  The helical hydrophobic moment: a measure of the amphiphilicity of a helix , 1982, Nature.

[101]  J. Fickett.  Recognition of protein coding regions in DNA sequences. , 1982, Nucleic acids research.

[102]  D. Penny,et al.  Branch and bound algorithms to determine minimal evolutionary trees , 1982 .

[103]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[104]  K. R. Woods,et al.  Prediction of protein antigenic determinants from amino acid sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[105]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[106]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[107]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[108]  Peter D. Moore,et al.  Reconstructing the past , 1979, Nature.

[109]  P. Y. Chou,et al.  Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .

[110]  M. Snyder,et al.  Reconstructing the Past: Some Cognitive Consequences of Person Perception , 1978 .

[111]  David F. Shanno,et al.  Conjugate Gradient Methods with Inexact Searches , 1978, Math. Oper. Res..

[112]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[113]  Donald E. Knuth,et al.  Fast Pattern Matching in Strings , 1977, SIAM J. Comput..

[114]  K. Tamm.  C. J. F. Böttcher: Theory of Electric Polarization, Vol. 1, 2. Auflage. Elsevier Scientific Publication Company 1973, 396 Seiten. Preis: Dfl 100,—. , 1974 .

[115]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[116]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[117]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[118]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[119]  H. Lehmann,et al.  Nucleic Acid Research , 1967 .

[120]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[121]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[122]  C. M. Reeves,et al.  Function minimization by conjugate gradients , 1964, Comput. J..

[123]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[124]  Soichi Wakatsuki.  Acta Crystallographica , 1948, Nature.

[125]  Journal of Chemical Physics , 1932, Nature.

[126]  Eric F Darve,et al.  Author ' s personal copy A hybrid method for the parallel computation of Green ’ s functions , 2009 .