Collaborative Science

Accelerating time to market and driving innovation with collaboration, knowledge based under-standing and prediction.

Macromolecule Design and Analysis

Determining the three-dimensional structure and properties of a macromolecule, such as enzymes, antibodies, DNA or RNA is a fundamental component to a wide range of research activities. Discovery Studio delivers a comprehensive portfolio of market leading, validated scientific tools, able to assist in every aspect of macromolecule-based research.

With Discovery Studio, you can rapidly and easily:

  • Perform multiple sequence alignments (BLAST and PSI-BLAST)
    • For antibodies and multiple chain proteins, simultaneously and independently perform multiple sequence alignments of each protein chain
  • Generate 3D structure models using MODELER
    • Analyze and clean-up models from 3D structure repositories (e.g., PDB)
    • Build homology models directly, from either sequence information or X-ray diffraction data
    • Use LOOPER to systematically search loop conformations and rank using CHARMm
    • Alternatively, graft loop conformations from a template structure onto a target model
    • Systematically optimize amino acid side-chains using ChiRotor CHARMm simulations
    • Predict the transmembrane helices in transmembrane protein sequences
    • Verify the quality of a structure model
  • Study macromolecule interactions with their partners
    • Use ZDOCK to perform protein-protein docking and predict protein binding partners
  • Conduct forcefield based simulations using CHARMm c41b1
    • Predict isoelectric point and pH dependent stability of protein
    • Predict protein ionization and protonate residues at a specified pH
    • Perform macromolecules simulations using explicit solvation models
    • Perform macromolecules simulations using implicit solvation or implicit membrane models
  • Predict effects of amino acid mutations on macromolecule properties
    • Impact on binding affinity
    • Temperature- or pH-based stability
    • Protein aggregation and developability
    • Identify stable disulfide bridge sites
  • Study Protein unfolding or conformational changes using CHARMm-based Steered Molecular Dynamics (SMD) simulations
  • Predict sites prone to Post Translational Modifications (PTMs) using sequence-based motif searching
  • Improve stability in a protein, by predicting disulfide bridges sites

Macromolecule Modeling Datasheet