Discovery Studio (DS) is a suite of software for modeling small and polymeric systems. It is developed and distributed by Dassault Systèmes BIOVIA (formerly Accellrys). This product suite features a robust academic collaboration program that supports scientific research and leverages many software algorithms originally developed in the scientific community, including CHARMM, MODELLER, DELPHI, ZDOCK, DMol3, and more. Key capabilities of DS currently include protein characterization (including protein-protein interactions), homology modeling, molecular mechanics calculations, and molecular dynamics simulations, structure-based drug design tools (including ligand-protein interactions, new drug design), molecular docking, small molecule-based drug design tools (including quantitative structure-activity relationship, pharmacophore, database screening, ADMET), design and analysis of combinatorial libraries. DS can be applied to the following research areas of life sciences: new drug discovery, bioinformatics, structural biology, enzymology, immunology, virology, genetics, and tumor research.
On the DS software platform, CD ComputaBio can provide customers with a full range of biopharmaceutical design support for performing hybrid QM/MM calculations, pharmacophore modeling, polymer design and validation, and more.
Homologous protein models are evaluated in DS mainly through Ramachandran plot and Profile-3D. Ramachandran plot is to evaluate the rationality of the backbone conformation of two adjacent peptide units by the minimum contact distance between non-bonded atoms in the protein and to represent the allowed and disallowed conformations in the protein. Profile-3D uses the 3D-1D scoring function to detect the matching relationship between the constructed model and its own amino acid sequence. The higher the score, the more reliable the homology model.
Fig 1. Antibody modeling sample
ADMET properties refer to the absorption, distribution, metabolism, excretion, and toxicity of molecules in the organism.
A pharmacophore is a collection of steric and electronic features necessary to ensure optimal molecular interaction with a specific biological target structure and trigger (or prevent) its biological response.
Amino acid site-directed mutagenesis of proteins can be used in the design of enzymes and antibodies to improve binding affinity.