Clote Lab

Computational Molecular Biology

1. http://arxiv.org/
2. http://front.math.ucdavis.edu/: portal to math arXiv.
3. Knowledge Web (for Medline, etc.)

1. Bioinformatics meetings
2. MIT Bioinformatics Seminar, co-organized by P. Clote (BC) and B. Berger (MIT)

1. LIGSITE: Dresden web site for protein-ligand docking using Connolly surfaces.
2. HEX: INRIA protein docking software, with associated web server.
3. GENO3D: Lyon server for protein homology modeling.
4. Swiss PDB Viewer
5. Los Alamos National Library HIV sequence database
7. MicroRNA databases
8. GRIMM-Synteny
9. OSfinder
10. Structure-Interaction Relational Database (SIRD)

1. LocARNA software for local alignment of RNA, developed by S. Will (Freiburg).
2. Vienna RNA Package: information on functions, developed by I. Hofacker (Vienna). Also here .
3. piRNA software from Simon Fraser University to compute partition function for RNA hybridization between two molecules.
4. RNAalign, paper by G. Blin, A. Denise, S. Dulucq, C. Herrbach, and H. Touzet, with software here.

1. Valgrind: debugger, manual, info.
2. JABREF java reference manager.
3. Ref2Bib reference manager.
4. www.whenago.com: Events of the past on certain days of the year.
5. PyLab
6. Matplotlib: Python code for 2D plotting
7. TAZ
8. Healthmap.org

1. myPresto: Tool for structure guided drug development.
2. SEQATOMs: web service to return sequence, structure, etc. for PDB files that properly treats missing residues. Article by Brandt et al. is here
3. Numerical software
4. Gnuplot Tutorial
5. Python Resources
6. PyDSTool: Python tool for (differential equation) dynamic systems.

Tools

1. MINRMS: computing RMSD between proteins.

Cloaking Link

1. http://www.the-cloak.com/anonymous-surfing-home.html: Link provided by governmental agency for use when anonymously testing web servers when reviewing grant proposals or journal submissions.