Analytical Services, Databases and Software (Award Period II)

Award Period: III| II | I

A. Subcellular Simulation Tools
APBS  Adaptive Poisson-Boltzman Solver (McCammon)
GAMESS  Quantum Mechanical Molecular Modeling (Baldridge)
PDB2PQR Server

Mirrors

  Enables conversion of PDB files into PQR files (N. Baker)

 Washington University, St. Louis
QMView  Quantum Mechanical Viewing Tool (Baldridge)

B. Sequence Analysis and Discovery Tools
CMSMBR  CMS Molecular Biology Resource (Smith)
Dictyostelium BLAST Search Tool   (Gribskov)
Euler  Genomic DNA fragment assembly tool
FPS  Family Pairwise Search Tool (Gribskov)
Homophila  Human Disease to Drosophila Gene Database (Gribskov)
NIH NCBI GenBank Mirror at NBCR   (NBCR)
MAST  Motif Alignment & Search Tool (Gribskov)
MEME  Multiple EM for Motif Elicitation (Gribskov)
MetaMEME  (Gribskov)
MIA  Molecular Information Agent (Gribskov)
MotifWeb  formerly SeqWeb (Down as of 8/26/04)
PlantsP  Functional Genomics of Plant Phosphorylation (Gribskov)
PlantsT  Functional Genomics of Plant Transporters (Gribskov)
PKR  Protein Kinase Resource
2HAPI  High-density Array Pattern Interpreter (Gribskov)

C. Structural Comparison and Analysis Tools

BioSync  Synchrotron Information Portal (NBCR)
CE  Combinatorial Extension (Bourne)
CKAAPS Database  (Bourne)
PAT  Proteins of Arabidopsis thaliana (Bourne)
SAT  Structure Alignment Tools (Ten Eyck)
SDSC1  Protein Structure Homology Modeling Server (Bourne)

D. Multiscale Visual Modeling Tools and Environments
AutoDock  (Olson)
AutoDock Viz. Environment ToolKit (ADT)   (Sanner/Olson)
MSMS  Maximal Speed Molecular Surface Calculator (Sanner/Olson)
PMV  Python Molecular Viewer (Sanner)  (Mgl Tools)
Vision  Visual Programming Environment (Sanner), including NetworkEditor

E. Cell and Organ Modeling Tools and Environments
Continuity 6.0  Continuum Modeling for Bioengineering & Physiology (McCulloch)
Render Mesh in Continuity 5.5  (McCulloch)
Cardiac Anatomy Models  (McCulloch)
Optical mapping image analysis in Continuity 5.5  (McCulloch)
Angles, Automated Measurement Of Orientation & Angular Deviation in Continuity 5.5  (McCulloch)
Cell Center Database  (Ellisman)
Telesciene Portal   (Ellisman)
 

This Resource is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant (P 41 RR08605) to researchers at the University of California, San Diego, including the San Diego Supercomputer Center (SDSC), the California Institute of Telecommunications and Information Technology (Calit2), The Center for Research in Biological Systems (CRBS), The Scripps Research Institute (TSRI), and Washington University in St. Louis (WUSTL).

Nation Center For
Research Resources

National Biomedical Computation Resource
University of California, San Diego
9500 Gilman Drive, MC 0440 - La Jolla, CA 92093-0440
Phone: (858) 534-5079 - Fax: (858) 534-5033
Email Us

National Institutes
of Health