Molecular Docking

• DOCK
• AutoDock
• GOLD
• Glide
• FlexX
• ICM
• Rosetta
• ClusPro
• FRED

File Format Conversion

• Babel
• BabelWin
• OpenBabel
• Mol2Mol

Ligand Conformer Generation

• OMEGA

• CORINA

Molecular Dynamics

• AMBER
• CHARMM

Molecular Modeling

• MODELLER
• SYBYL
• SCWRL
• SWISS-MODEL
• WHAT IF

Model Evaluation

• PROCHECK
• WHATCHECK

Molecular Visualization/Analysis

• Chimera
• RasMol 
• Prorein Explore
• Swiss-PdbViewer
• VMD
• MOLMOL
• MolScript
• Raster3D

Database Searching by Sequence Similarity

• BLAST @ NCBI
• PSI-BLAST @ NCBI
• FASTA @ EBI

• T-COFFEE - multiple sequence alignment
• ClustalW @ EBI - multiple sequence alignment
• SPEM - multiple sequence alignment
• DiAlign - multiple sequence alignment

Structure Alignment

• MatchMaker tool in Chimera - pairwise
• FAST - pairwise; paper compares the method to DaliLite, CE, and K2
• MultiProt - truly multiple rather than assembly of pairwise alignments
• SuperPose - multiple
• SALIGN  - multiple
• K2, K2SA - pairwise
• CE (pairwise), CE-MC (multiple, building upon pairwise CE alignments)
• DaliLite - pairwise
• Protein3Dfit - pairwise

• PDB - protein 3D structure database
• RasMol / Protein Explorer - molecule 3D structure viewers
• SCOP - Structural Classification Of Proteins
• The DALI Domain Database
• FSSP - fold classification based on structure-structure alignment of proteins

• PubMed
• Scopus
• BioMedSearch
• ISI Web of Science search

• Annual Reviews of Biochemistry

• Annual Reviews of Biophysics and Biomolecular Structure

• Biochemistry

• Bioinformatics

• Biophysical Journal

• Biopolymers

• Current Opinion in Drug Discovery & Development

• Current Opinion in Structural Biology

• Journal of the American Chemical Society

• Journal of Biological Chemistry

• Journal of Chemical Information and Modeling

• Journal of Chemical Physics

• Journal of Chemical Theory and Computation

• Journal of Computational Chemistry

• Journal of Computer-Aided Molecular Design

• Journal of General Physiology

• Journal of Medicinal Chemistry

• Journal of Molecular Biology

• Journal of Molecular Graphics and Modelling

• Journal of Physical Chemistry B

• Journal of Physiology

• Nature

• Nature Reviews Drug Discovery

• Nature Structural Biology

• Nucleic Acids Research

• Proceedings of the National Academy of Sciences of the USA

• Protein Science

• PROTEINS: Structure, Function, and Bioinformatics

• Physical Review E

• Physical Review Letters

• Science