Bioinformatics Analysis Tools Links

BioTech FYI Center - Resources

Analyse & Model 3D Structure

3D Viewers
RasMol (Free offline 3D viewer. Download ) Chime (Browser plugin for structure view from MDL Chemscape) Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)	Swiss-Pdb Viewer (Deep View) (Free offline 3D viewing and analysis application, tightly linked to Swiss-Model . Tutorial ) WebMol (Online 3D viewer at University of California, USA) WebMol (Online 3D viewer at EMBL)

3D Analysis

TOPS (Protein topology cartoon generation at EBI, UK)
3DB Browser (Structure database browser at Weizmann Institute of Science, Israel)
STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)
Predicting Protein 3D structure based on homologous sequence search (EMBL Heidelberg, Germany)
LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
VAST (Structure-structure similarity search at NCBI, US)
ASC (Analytic Surface Calculation of PDB molecules at EMBL, Heidelberg)
Protein-Protein Interaction Server (UCL, UK)

DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
GenTHREADER (Sequence profile based fold recognition on PSIpred server at Brunel University, UK)
123 (Fold prediction by aligning (threading) to a (set of) structure(s)
DALI (Automated Protein Structure Alignment at EBI,UK)
LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
MolSurfer (Calculate and navigate protein-protein interfaces at EMBL, Heidelberg)

3D Homology Modelling
CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark) 3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland) SDSC1 (Protein structure homology modeling server at SDSC, USA) List of comparative modeling tools (at the Rockefeller University, NY, USA)	Swiss-Model (Automated protein modeling server at ExPASy, Switzerland) FAMS (Fully Automated Modeling Service at Kitasato University, JP) 3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK ) Meta PP (Collection of structure prediction services at Columbia University, USA)

Bioinformatics Analysis Tools Links