Analyse & Model 3D Structure

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)
• PsiPred (Sequence profile based fold recognition at Brunel University, UK)
• 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)
• OCA (Structure database browser 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)
• 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)
• List of comparative modeling tools (at the Rockefeller University, NY, USA)