Information Page. A List of Secondary Structure Prediction Servers

Transcription

1 Introduction to Bioinformatics Information Page Chapter 5, page 1/4, 2012/11/09 A List of Secondary Structure Prediction Servers Name APSSP PredictProtein GOR IV Jpred 3 CFSSP NNPREDICT JUFO BCM Search Launcher URL A List of 3D Molecular Viewer Jmol free RasMol free CanVasMol free Cn3D free Molegro free MGL Tools free Swiss-PDBViewer free Maestro free JMV free VMD free PyMOL commercial

2 A List of Protein Structure Prediction Servers I-TASSER Multiple-Threading QUARK AB Initio Swiss-Model Homology Modeling Modeller Homology Modeling / Threading Robetta AB Initio + Homology Modeling pgenthreader Threading RAPTOR Threading PEP-FOLD AB Inito ModLoop AB initio A list of Model Quality Assessment Programs Name PROCHECK Verify_3D WHAT_CHECK ERRAT PROVE ProQ MetaMQAPII ModFOLD QMEAN Anolea Prosa web URL A list of Protein-Protein & Protein-Ligand Docking Software GRAMM du/main/resources_gramm1.03. php Global Range Molecular Matching, The program performs an exhaustive 6-dimensional search. ZDOCK ZDOCK is a Fast Fourier Transform based protein docking program. ICM-Docking ligand-protein docking, peptide- protein docking, and protein-protein docking, including interactive graphics tools PatchDoc hdock Molecular Docking Algorithm Based on Shape Complementarity Principles

3 A List of Protein-Ligand Docking Software AutoDock automated docking of flexible ligands to macromolecules, designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure (free) DockVision docking package created by scientists for scientists by including Monte Carlo, Genetic Algorithm, and database screening docking algorithms FRED Fast Rigid Exhaustive Docking, multi-conformer docking program (commercial) FlexX index.html?ct=1 fast computer program for predicting protein-ligand interactions, complex prediction and virtual screening, conformational flexibility of the ligand; rigid protein (commercial) Glide oducts/14/5 high-throughput ligand-receptor docking for fast library screening, fast and accurate docking program, identifies the best binding mode through Monte Carlo sampling, provides an accurate scoring function for ranking of binding affinities (commercial) GOLD ducts/life_sciences/gold calculating docking modes of small molecules into protein binding sites, genetic algorithm for protein-ligand docking, full ligand and partial protein flexibility, virtual library screening hint! Hydropathic INTeractions, empirical molecular modeling system with new methods for de novo drug design and protein or nucleic acid structural analysis, calculates 3D hydropathy fields and 3D hydropathic interaction maps, evaluates/predicts effects of site-directed mutagenesis on protein structure and stability VEGA calculation of ligand-receptor interaction energy

4 A list of Protein-Protein Docking Software 3D-Dock Suite 3D-Gardon Bielefeld Protein Docking DOT ESCHER NG FireDock HADDOCK GrammX uk/docking uk/~3dgarden/ elefeld.de/~posch/dock ING/install.html MS/DOT escherng/index.htm il/firedock/ nl/haddock/ cs.ku.edu/resources/gra mm/grammx incorporating FTDock (Fourier Transform Dock), RPScore (Residue level Pair potential Score) and MultiDock (Multiple copy side-chain refinement Dock) system for modeling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm detects geometrical and chemical complementarities between surfaces of proteins and estimates docking positions Daughter Of TURNIP, computation of the electrostatic potential energy between two proteins or other charged molecules new release, with a reengineered code, includes some new features: protein- protein and DNA-protein docking capability; fast surface calculation based on the NSC algorithm Fast Interaction REfinement in molecular DOCKing, web server for flexible refinement and scoring of protein-protein docking solutions High Ambiguity Driven protein-protein Docking, biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data introduced as ambiguous interaction restraints (AIRs) to drive the docking process This software is different from the original GRAMM, except that both packages use FFT for the global search of the best rigid body conformations. HEX Hex is an interactive protein docking and molecular superposition program. RosettaDoc b.jhu.edu/ predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation

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