AUTODOCK:


AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.
AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids.
In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.
AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.
We have also developed a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.

AutoDock has applications in: X-ray crystallography; structure-based drug design; lead optimization; virtual screening (HTS); combinatorial library design; protein-protein docking; chemical mechanism studies.

AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution. Click on the "Downloads" tab. And Happy Docking!

 

Bioinformatics Books

Sequence Analysis and General Bioinformatics   BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley & Sons Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: A Primer, Charles Staben, 2001, Jones & Bartlett Pub Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley & Sons Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc. Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub. Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman & Hall Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society Mathematical Methods for DNA Sequences

Inspirational Software for Biologists

Geneious Pro is a revolutionary bioinformatics software platform that is both ultra-powerful and easy to use. Scientists, researchers and students are able to search, organize and analyze genomic and protein information via a single desktop program that provides publication ready images to enhance the impact of your research.

 

http://www.geneious.com/

Bioinformatics Software and Tools 1. Gene Predictor(ChemGenome 2.0) Whole Genome Analysis 2. Bhageerath Predicts native-like structures for small globular proteins 3. Sanjeevini A complete drug design software. 4. Binding Affinity Prediction of Protein-Ligand Server(BAPPL) Computes the binding free energy of a protein-ligand complex. 5. Binding Affinity Prediction of Protein-Ligand complex containing Zinc Server (BAPPL-Z) Computes the binding free energy of a metalloprotein-ligand complex containing zinc. 6. Drug-DNA Interaction Energy (PreDDICTA) Calculates the Drug-DNA interaction energy. 7. ParDOCK - Automated Server for Rigid Docking Predicts the binding mode of the ligand in receptor target site. 8. Active Site Prediction 9. Automated Version Of Active Site Prediction (AADS) Predicts 10 binding sites in a protein target and docks the uploaded ligand molecule at all 10 sites predicted in an automated mode. 10. DnaDOCK - Dna Ligand Docking All-atom energy based Monte Carlo DNA ligand docking 11. Non Redundant Database of Small Molecules Virtual high throughput screening of small molecules and their optimization into lead like candidates. 12. Lipinski Filters Checks whether a drug satisfies the 5 Lipinski rules. 13. DNA Sequence to Structure Generates double helical secondary structure of DNA using conformational parameters taken from experimental fiber-diffraction studies. 14. Hydrogen Addition to Nucleic Acid Adds the hydrogen coordinates to the X-ray crystal structures of Nucleic acids 15. Hydrogen Addition to Protein Adds the hydrogen coordinates to the X-ray crystal structures of Proteins. 16. Gene Evaluator(ChemGenome 1.1) Characterizes a DNA sequence as gene or nongene 17. Protein Structure Generation Structure Generation from given dihedrals 18. Persistence Length Filters for Globular Protein Evaluation 19. Radius of Gyration Filters for Globular Protein Evaluation 20. Hydrophobicity Filters for Globular Protein Evaluation 21. Packing Fraction Filters for Globular Protein Evaluation 22. ProRegIn Protein Regularity Index 23. Protein structure optimizer Energy minimizer for proteins 24. ProSEE Scoring Function for Protein Structure Evaluation Calculates intramolecular energy of a protein in component-wise break up. 25. Superimpose Fits two molecules and calculates the RMSD between them. 26. Protein Angle Descriptor Calculates the angles & dihedral in the main chain of the protein 27. Wiener Index Calculator This tool is useful for calculating Wiener index. 28. RASPD for Preliminary Screening of Drugs This tool is useful for preliminary screening of drug molecules based on Wiener index calculation. This will predict binding energy of drug/target at a preliminary stage. 29. BGPred(Beta Gamma Turn Predictor) BG Pred web server predicts beta and gamma turns. 30. Volume Calculator Calculates the volume of a molecule 31. Melting Temperature Predictor (For oligonuclotide) It predicts the melting temperature of short DNA sequences (upto 70 base pairs) at a user defined salt within the specified range. 32. Genome analysis by melting It predicts the melting temperature for longer(>70 bases) DNA sequences, and it also gives the melting profile for the sequence. 33. Transferrable Partial Atomic Charge Model - up to 4 bonds (TPACM4) This tool is used for assignment of partial atomic charge of small molecules. 34. PROSECSC PROTEIN SECONDARY STRUCTURE PREDICTION. 35. Gene Predictor(ChemGenome 3.0) ChemGenome 3.0 is a gene prediction tool that takes a whole genome sequence or a part of the genome of a prokaryote or virus as input and predicts genes along with their coressponding protein sequences in all the six reading frames. 36.Bhageerath H A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction. Starting with sequence, the web server predicts 5 native-like candidate structures for the protein. 37. pcSM Software pcSM: Capturing Native Protein Structures with a Physico-Chemical Metric.