BOL

An ultra–high-performance protein–protein docking software for heterogeneous supercomputers Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics...

A useful blog at http://molecularmodelingbasics.blogspot.in/

This Molecular Structure Modeling Tutorial is usefule for beginners http://www.chem.ucla.edu/harding/tutorials/models/models02.pdf

AutoDock VINA is an open-source program for doing molecular docking http://vina.scripps.edu/index.html

The new version of Modeller, 9.13, is now available for download!

Following are the list of In-silico Binding Site Prediction in Proteins tools CASTp : http://sts.bioengr.uic.edu/castp/  Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and...

Pharmaceutical bioinformatics is a new discipline in the area of the genomics revolution. It is central to biomedicine with application in areas like pharmacy, medicine, biology and medicinal chemistry. http://www.pharmbio.org/

Molecular Conformation Dynamics andComputational Drug Design http://opus4.kobv.de/opus4-zib/files/742/ZR-03-20.pdf

Computer-aided drug design platform using PyMOL User Guide http://people.pharmacy.purdue.edu/~mlill/software/pymol_plugins/Manual_010612.pdf

Using AutoDock 4 with  AutoDockTools: A Tutorial  Written by Ruth Huey and Garrett M. Morris http://dasher.wustl.edu/chem478/software/autodock-tutorial.pdf

ISOA/ARF Drug Development Tutorial  By Jens Eckstein http://www.alzforum.org/drg/tut/ISOATutorial.pdf

Molecular Modelling for Beginners by Alan Hinchliffe ftp://ftp.cecalc.ula.ve/bioinfo/CD-THAS/Presentaciones/modelado/MMFB.pdf

DST-SERB Winter School on Computational Chemistry

Protein-Ligand Docking for Drug Design by Sam Z. Grinter http://web.missouri.edu/~szg4y4/presentation3.pdf

Molecular docking tutorial with Arguslab http://www.ffa.uni-lj.si/fileadmin/datoteke/FK/Gradiva_FK/2011-12/Seminarji/Arguslab_navodila.pdf

One of my favourite docking tutorial http://www.molvis.indiana.edu/C687_S99/docking.html

Quick­start guide to protein­ligand docking using Rosetta 3.1 http://www.meilerlab.org/jobs/downloadfile/name/rosetta3_ligand_docking.pdf Ptotein logand docking...

  An informative tutorial for beginners ... http://www.chem.ox.ac.uk/course/cache/

The Rosetta macromolecular modeling, prediction, and design software suite is supported by a large developer community and enjoys a diverse user base. Each year Rosetta developers and users from academia and industry meet to discuss improvements and...