Web servers for Docking

• Cluspro 2.0 (PIPER)   Boston University and Stony Brook University, Massachusetts, U.S.
  Note: Really easy to use. Just click: Use the server without the benefits of your own account"
  
  
• LzerD   Kihara Lab, Purdue University, Indiana, U.S.
  Note: A bit more complex to use but it is still possible to submit two ".pdb" files and ignore the rest.
  
  
• LightDock Server    I believe, it is Barcelona, Spain.
  Note: This may require you to modify original ".pdb" files because the chain IDs MUST not overlap..
  Usage: How to Install

Free software for Docking

• MEGADOCK   Akiyama Lab, Tokyo Institute of Technology, Japan
  Note: I installed MEGADOCK under my account on ijcuster. No root access required and you can ask Dylan for help.
  Usage: How to Install & How to Run
  
  

Proteins Visualization software

• ChimeraX   University of California, San Francisco (UCSF)
  Usage: How to Install
  UCSF Chimera Documentation Index (look for section: Chimera Programmer's Guide)
  Preparing Molecules for DOCKing (This tutorial uses the program Chimera)
  ChimeraX Tutorial: Loop Modeling (look for section: Modeling a Missing Segment)
  Protein Docking: DockPrep - Python Script (Script !!!)
  
  
• PDB: Mol* 3D Viewer  (online viewer)
  Usage
  
  

Molecular Dynamic software

• Molecular Dynamics (MD) (free reading)  Start here.
  
  
• NAMD (free software)  Proprietary, free academic use. Theoretical and Computational Biophysics Group. University of Illinois, U.S.
  - Web    NAMD tutorial    (basic molecular dynamics simulations)
  - Web    NAMD tutorial (Ohio State University)    (Hands-on Introduction to Protein Simulations)
  
  
• GROMACS (free software)  Free and Open-source software. GROMACS development team is all over the world.
  Usage: How to Install
  - Web    How to run a Molecular Dynamics simulation using GROMACS    (GROMACS basic functions and commands)
  - Web    GROMACS Tutorial: Molecular Dynamics simulation of a protein in water environment
  - Web    Official GROMACS Tutorials by Justin A. Lemkul, PhD, Virginia Tech Department of Biochemistry
  
  

My Projects software

• InI-Max (my software)  Decoy contact Signatures.
  - Commands    ChimeraX, Commands, InI_Sets, InI_Delta
  
  

MISC

• PDB file format (document)  protein data bank file format
  - Web    specs
  
  
• Levels of Protein Organization (Secondary Structure) (document)  protein data bank file format
  - Web    specs
  
  
• Kevin X (data)  empty
  - Google drive    docking results.
  
  
• Slurm (data)  empty
  - Web    Useful Slurm commands
  srun --cpus-per-task 4 --pty bash -i   (will get you on a COMPUTE NODE)