Cluster usage: (short) tutorial/documentation

Secondary Structure Prediction:

• Dali server: 3D comparison
• DSSP (W. Kabsch)
• GCG
• NPSA (consensus secondary structure prediction)
• The PredictProtein server (PHD, TOPITS, MaxHom, EvalSec)
• PROFIT (Protein Fold Indentification Tool)
• Structural Databases and Servers
• SOSUI (secondary structure prediction for membrane proteins)

Homology modeling:

Protein Modeling

• WIWWWI server
• SCWRL server
• 3D JIGSAW server
• SWISS MODEL server
• Small Disulphide-bonded Proteins Modeling server
• MOD-WEB server

• BIOMER java
• 3DNA
• MFOLD

• VADAR

Crystallography:

• ARP/wARP (Automatic Refinement Program)
• ACORN (ab initio procedure for the determination of protein structure at atomic resolution.)
• ALIGN (Aligns two coordinate sets)
• CCP4
• CNS (Crystallography and NMR System)
• DATAMAN (Reflections Manipulation)
• DDQ (Difference Density Quality: Structure Validation Tool)
• DENZO (Detector Data Processing)
• DM Density modification
• EPMR (Evolutionary Programing for Molecular Replacement)
• ERRAT (Model Analyzer)
• ESCET(Helps determine conformationally invariable regions of protein given multiple crystal structures.)
• Ezprot (Analysis of Protein Sequence and Structure)
• Gerard's Programs (Moleman, Rave, Voidoo, Pacman)
• HEAVY
• MAID
• MAPMAN (Maps Manipulation)
• MAPS (Multiple ALignment of Protein Structures)
• Matthew's coefficent calculator
• NIST*LATTICE (Analysis of Lattice Relationships)
• PARVATI(Protein Anisotropic Refinement Validation and Analysis Tool)
• PDB_EXTRACTextract PDB deposition info from log files
• PHASER Maximum likelihood molecular replacement
• PROCHECK (Stereochemistry quality checker)
• PRODRG: Generate Topology files for CNS, O, and SHELX
• PROVE Structure Validation using atomic volumes.
• RAVE (Real Space Averaging)
• SHAKE & BAKE Find heavy atom positions from isomorophous and/or anomalous coefficients
• SHELXL
• SITUS Docks crystal structures into EM maps
• Space Group Symmetry Operators and Diagrams
• SOLVE (Automated crystallographic structure solution for MIR and MAD)
• STACCATO Makes a sequence alignment from a collection of aligned PDB files
• WHAT_CHECK (Stereochemistry quality checker)
• XDS
• XPLOR 3.8

Graphics:

• AUTODOCK (Docks a ligand into a crystal structure using a Lamarkian genetic algorithm.)
• BIOSYM
• DOCK
• GRASP
• Kinemage, Probe, Reduce (Richardson's Programs)
• MSP (Molecular Surface Package by Michael Connolly)
• Mathematica
• Midas
• MolMol
• MolScript
• O Ono (Alwyn Jones) see also AtoZ of O and O for morons
• RasMol
• RIBBONS (By Mike Carson)
• Raster3D and ImageMagick
• Setor (by Stephen Evans)
• TOPS (topology diagrams) downloaded from the TOPS web page for both Linux and DEC
• TopDraw (topology diagrams)
• XMGR (Xwindows plotting)
• XtalView

Programming:

• The *Bioperl* Project an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
• Numerical Recipes (C and FORTRAN)
• LINPACK (Linear Algebra Soubroutine Package)
• IBM Scientific Soubroutine Package

Molecular Dynamics and Simulations:

• CHARMM Chemistry at HARvard Macromolecular Mechanics (on linux)
• AMBER Assisted Model Building with Energy Refinement (on linux)
• RosettaDesign Finds low free energy sequences for target protein backbones.
• RosettaAbInitio Based on the ROSETTA method for ab initio protein structure prediction, which produced de novo structure predictions of unprecedented accuracy in the CASP4 international blind test of protein structure prediction methods. (on linux)

Assorted PC/MAC Software:

• PPP for MACs (Only for local users)

NMR:

• NMRPipe (a multidimensional spectral processing system )