Macromolecular Modeling and Simulation

SYBYL Provides Tools for Modeling Biological Macromolecules

Understanding and modeling the static and dynamic 3D structural properties of biological macromolecules is an important basis for structure based design activities and can uncover likely biological functions. SYBYL-X applies homolog recognition, structure and function prediction from sequence, energetic and dynamic simulation, ligand binding site analysis, and 3D modeling techniques in workflow-centric applications that address critical structural biology design tasks, such as macromolecular modeling and bioinformatics analysis.

SYBYL-X users can:

  • Build 3D models from the amino acid sequence– the basis of further structure based design activities
  • Understand the conformational and energetic properties of macromolecular targets
  • Assess receptor flexibility and its impact on ligand recognition or receptor activation

The SYBYL-X Suite includes:

  • Advanced Protein Modeling (APM) for protein homology modeling enables users to perform both homolog finding and comparative modeling through a streamlined interface. APM finds relevant homologs to start the modeling process by taking advantage of environment-specific substitution tables, structure-dependent gap penalties, automated alignment method selection, and the highly annotated HOMSTRAD database. Homologs are structurally aligned based using homology and local structural environment, and then structurally conserved regions are identified using backbone curvature and torsion in addition to C-alpha rmsd and homology. Loops (structurally variable regions) are then modeled by knowledge-based or ab initio approaches, and sidechains are added by enumerating rotamer combinations constrained by borrowing as much information from the parent homologs as possible. A range of analysis tools are available to highlight potential problems with the structure and allow the user to iterate through the process and refine initial models.
  • MOLCAD and MOLCAD Plus create graphical images that reveal the properties of molecules essential for molecular recognition. MOLCAD calculates and displays the surfaces of both small molecule drugs and macromolecular targets and can identify channels and cavities that may be potential binding sites. A broad range of properties can be mapped onto these surfaces to rationalize the properties of the binding site and ligand/receptor complementarity.

Learn more about the SYBYL-X Suite:

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