BioNavigatoroinformatics workspace


Molecular modeling
Molecular modeling and the ability to derive a better understanding of structure-function relationships in proteins is contributing to rapid advances in fields such as drug design

This release of BioNavigator provides this functionality by incorporating many programs including WHAT IF and ICM Homology Modeling. These programs are, as with all programs and databases in BioNavigator integrated seamlessly into the easy-to-use interface. Additionally there are 6 molecular modeling protocols included in BioNavigator that provide a step-by-step guide to carrying out common molecular modeling analyses, such as:

  • Contact Analysis
  • Find a Homologous PDB Structure
  • Homology Modeling
  • Protein Engineering
  • Protein Structure Mutation
  • Structure Analysis

What is molecular modeling?

Molecular modeling, within BioNavigator, is used for the analysis, modification, building and display of protein structures. It has applications in structure analysis such as determining contacts between the protein of interest and e.g. a drug; in protein engineering where residues are mutated to perhaps stabilize the structure;and homology modeling, where a three dimensional (3D) structure of a protein, with unknown structure, is built using a homologous protein as a template.

Figure: Structure of Lysozyme (PDB: 1l00) generated using ICM and displaying two active site residues and cysteine-97 complexed with Beta-Mercaptoethanol.

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