1. Structural Bioinformatics, Bourne & Weissig, Wiley-Liss, ISBN 0-471-20199-5
2. Protein Structure Prediction, Tramontano, Wiley-VCH, ISBN 3-527-31167-X
3. Protein Bioinformatics, Eidhammer, Jonassen, Taylor, Wiley, ISBN 0-470-84839-1
   

• There will be discussion forum created within the departmental dropbox
  

• DNA Databank of Japan (DDBJ)
• European Bioinformatics Institute (EBI)
• National Center for Biotechnology Information (NCBI)

• Protein Data Bank (PDB)
  
• Basic Local Alignment Tool (BLAST) with interfaces NCBI(USA), Pasteur Inst(France)
  
• Implementations of FASTA (Pearson and Lipman) sequence alignment method at IUBio(USA), GeorgetownU(USA), Pasteur Inst(France)
  
• Class, architecture, topology and homologous (CATH) superfamily
  
• Comparison of protein structures in 3D: DALI
  
• NIGMS structural genomics initiatives
  

• Rasmol
• PyMOL
• VMD
• MolMol.
  
• Ubuntu version here (Thanks to Mr. Arjang Fahim)
• Our executable, and the corresponding library file (both are required)
  
• This software will be demonstrated and used in this class.
• XPLOR-NIH.
  

• MolMol Script 1 (select atom)
• MolMol Script 2 (select residue)
• MolMol Script 3 (select and set angles)
• MolMol script for finding RMSD between two structures
• Xplor script for generating PDB and PSF file (all hydrogen atoms)
• Xplor script for evaluating energy of a structure.
  
• Xplor script for energy minimization (all atoms)
• Xplor script for energy minimization (fixed residues)
• Xplor script for energy minimization (rigid body minimization)
• Xplor script for dynamic verlet simulation with B-M initial velocities
• Xplor script for dynamic verlet simulation with fixed velocities
  

• Translation of cDNA sequence
  • ExPASY. You should be able to do most other things here.
    
• Sequence Homology
  • Blast at NCBI
• Secondary structure prediction
  • ExPASY. I recommend either PSIpred, PHD or HNN.
• Tertiary structure prediction
  • ExPASY.  I recommend using Rosetta or GenThreader.
• Structure validation
  • ExPASY.  Use Biotech Validation Suite for Protein Structures or PROCHECK. A limited versionof PROCHECK validation can be accessed through the pdb web site here.
    
  • When using the above site through PDB web, use the NMR option.
  • Most of what is needed for this project can be done manually in MOLMOL as listed below.
    • To add missing atoms such as hydrogen atoms: calcatom "H*"
    • To select bond lenghts: selectbond 'atom1.name="N" and atom2.name="HN"' followed by listselectedbond
    • To observe the Ramachandran space click on Fig and select Ramachandran. Make sure you select the appropriate background.
    • To assess VDW violations click on Calc-VanderWaals, select threshold of 0.0 and plot histogram. Note that before doing this, your entire molecule needs to be selected.
    • To compare the backbone (bb) rmsd between two structures use Options-Dialogs-RMSD function of MolMol. You need to select the same number of residues between the two structures. This function may fail after repeated number of used. Then, quit out of the program and restart or you can use the command line option of the function. To match residues 1-25 of protein 1 and 70-94 of protein 2 you need to type the following two commands:
      • SelectAtom 'bb & (#1:1-25 or #2:70-94)'
      • fit to_first 'selected'
      • rmsd will show on the bottom of the page and the two structures will be superimposed.
      • Note that if one of your structures contains an ensemble of structures, you can just work with the first instance and delete the rest.
        
• Functional analysis
  • Establish function based on structural similarity. Do not do this exclusively based on sequence homology. Use DALI to get structurally similar proteins.

• Align two sequences (bl2seq)
• DaliLite:  Pairwise comparison of protein structures
• Our USC, home-grown TALI

The following topics will be  presented :

• Introduction to biochemistry of amino acids and protein.
• Introduction to programming in PERL.
  
• Introduction to biomolecular visualization tools.
  
• Topics in protein structure characterization and classification.
• Topics in experimental data (NOE and RDC data from NMR).
  
• Computational protein folding by force field minimization and constrained optimization.
• Protein folding based on threading algorithms.
• Topics in molecular modeling, molecular mechanics and quantum mechanics.
  
• Topics in molecular encoders/decoders.