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 new code, as well as exciting, emerging applications.
This Collection draws from material presented at RosettaCon 2012. The Collection is meant to both highlight new scientific developments within the Rosetta community and provide a rigorously reproducible workflow for each protocol. This year's Collection highlights exciting advances that increase the usability of Rosetta, improve current methods, and introduce completely new protocols.
More @ http://www.ploscollections.org/article/browse/issue/info:doi/10.1371/issue.pcol.v02.i21
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An informative tutorial for beginners ... http://www.chem.ox.ac.uk/course/cache/
Quickstart guide to proteinligand docking using Rosetta 3.1
http://www.meilerlab.org/jobs/downloadfile/name/rosetta3_ligand_docking.pdf
Ptotein logand docking tutorial
https://www.cs.princeton.edu/courses/archive/fall05/cos597A/lectures/docking1.pdf
One of my favourite docking tutorial http://www.molvis.indiana.edu/C687_S99/docking.html
Molecular docking tutorial with Arguslab http://www.ffa.uni-lj.si/fileadmin/datoteke/FK/Gradiva_FK/2011-12/Seminarji/Arguslab_navodila.pdf
Protein-Ligand Docking for Drug Design by Sam Z. Grinter
http://web.missouri.edu/~szg4y4/presentation3.pdf
Molecular Modelling for Beginners by Alan Hinchliffe ftp://ftp.cecalc.ula.ve/bioinfo/CD-THAS/Presentaciones/modelado/MMFB.pdf
ISOA/ARF Drug Development Tutorial By Jens Eckstein http://www.alzforum.org/drg/tut/ISOATutorial.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
Computer-aided drug design platform using PyMOL User Guide http://people.pharmacy.purdue.edu/~mlill/software/pymol_plugins/Manual_010612.pdf
Molecular Conformation Dynamics andComputational Drug Design http://opus4.kobv.de/opus4-zib/files/742/ZR-03-20.pdf
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/
AutoDock VINA is an open-source program for doing molecular docking http://vina.scripps.edu/index.html
This Molecular Structure Modeling Tutorial is usefule for beginners http://www.chem.ucla.edu/harding/tutorials/models/models02.pdf
A useful blog at http://molecularmodelingbasics.blogspot.in/