Enhance Macromolecule-Based Research

Determining the three-dimensional structure and properties of macromolecules, such as enzymes and antibodies, is a fundamental component to a wide range of research activities. For example, different conformations which arise from normal molecular dynamics or interactions with ligands or other proteins may reveal novel binding sites or provide clues as to its function. While thousands of molecules have had their structures resolved experimentally, obtaining high fidelity structural data remains a nontrivial process.

Simulation can augment physical experimentation by providing insight into macromolecular structure. Additionally, techniques such as homology modeling can help predict structural models for novel molecules, guiding therapeutic design and protein engineering efforts. BIOVIA Discovery Studio delivers a comprehensive portfolio of market leading, validated scientific tools, able to assist in every aspect of macromolecule-based research.

Search

  • Perform multiple sequence searches using BLAST and PSI-BLAST against local or NCBI databases
  • For multiple chain proteins, simultaneously and independently perform multiple sequence alignments of each protein chain
  • Predict the transmembrane helices in transmembrane protein sequences
  • Predict sites prone to Post Translational Modifications (PTMs) using sequence-based motif searching

Model

  • Analyze and prepare structures from 3D structure repositories (e.g., PDB)
  • Generate 3D structure models using MODELER
  • Verify the quality of a structure model
  • Use LOOPER to systematically search loop conformations and rank using CHARMm
  • Graft loop conformations from a template structure onto a target model
  • Systematically optimize amino acid side-chains using ChiRotor CHARMm simulations
  • Use ZDOCK to perform protein-protein docking and examine binding partner interactions
  • Study conformational flexibility with explicit solvent-based Molecular Dynamics (MD) simulations using CHARMm or NAMD   

Design

  • Predict electrical properties of the protein, including pH-dependent stability and protonation states and the isoelectric point
  • Conduct thermal or pH-based mutational stability and binding affinity predictions
  • Identify potential stable disulfide bridge locations
  • Calculate biophysical properties important for protein formulation, including viscosity and solubility

Start Your Journey

Accelerate your drug discovery with BIOVIA Discovery Studio. 

Join the conversation in the BIOVIA Drug Discovery & Development Community!

Also Discover

simulations discovery studio > Dassault systemes
Simulations
Protocols for State-of-the-art Molecular Dynamics Simulations 
BIOVIA pharmacophore design > Dassault Systemes
Ligand- and Pharmacophore-based Design
De Novo Drug Design, Multi-Target Drug Design and Activity Profiling
antibody solubility modeling > Dassault systemes
Biotherapeutics and Antibody Modeling
A Rich Set of In Silico Tools to Support The Design of Biotherapeutics
discovery studio SBBD > Dassault systemes
Structure-based Design
Comprehensive, Scalable Portfolio of Scientific Tools to Support Structure-based and Fragment-based Design
QSAR admet toxology > Dassault systemes
QSAR, ADMET & Predictive Toxicology
Tools for Designing Therapeutics with Favorable Pharmacokinetic Properties and Safety Profiles 
visualization discovery studio > Dassault Systemes
Visualization
Free, Feature-Rich Molecular Visualizer
BIOVIA Discovery Studio > Dassault Systemes
BIOVIA Discovery Studio
Comprehensive Modeling and Simulation for Life Sciences Research
BIOVIA Biosciences > Dassault Systemes
Biosciences
Accelerate Innovation in Life Sciences Research and Development

Learn What BIOVIA Can Do for You

Speak with a BIOVIA expert to learn how our solutions enable seamless collaboration and sustainable innovation at organizations of every size.

Get Started

Courses and classes are available for students, academia, professionals and companies. Find the right BIOVIA training for you. 

Get Help

Find information on software & hardware certification, software downloads, user documentation, support contact and services offering