Applications of SYBYL Software

SYBYL is a fully integrated computational chemistry and molecular simulation environment, providing a basis for understanding molecular structure and properties, especially the properties of new chemical entities. SYBYL is a comprehensive molecular simulation software developed by Trepos in the United States for the field of small drug molecules and biomacromolecules. SYBYL software can be used to simulate and score the docking of aptamers and small molecules. SYBYL software has its own scoring function Total-Score, which can be used to evaluate the result of each molecular docking. Since SYBYL consists of nearly 50 modules, the research that can be carried out includes modeling of small drug molecules, conformation analysis, three-dimensional quantitative structure-activity relationship research, pharmacophore modeling, virtual screening, homology modeling of biological macromolecules, activity Locus analysis, database search, etc.

Our Services Based on SYBYL Software

On the SYBYL software platform, CD ComputaBio can provide the listed services:

• Small Molecule Preparation
• Small molecule construction, preservation, molecular conversion between different formats
• Construction of mdb database, preparation of small molecules for different research purposes
• Optimization of molecules under different positions to find low-energy conformations
• Small molecule conformational search for active conformations
• Protein Preparation
• Target structure analysis/repair, protein structure characterization, protein loop repairment
• Construction, replacement and mutation of polypeptides
• Addition of molecular surface properties
• Amino acid residue selection, labeling, measurement of distance angles, etc.
• Drug Design
• Receptor-based molecular docking and virtual screening, de novo drug design
• Ligand-based QSAR, pharmacophore modeling and virtual screening, ligand-based virtual screening
• Biomacromolecule homology modeling
• Combinatorial library design and optimization
• Compound management
• Molecular Docking
  Surflex-Dock GenomX contains four molecular docking modes, and the scientists at CD ComputaBio can realize special docking modes such as protein flexible docking, restriction docking, and DNA-targeted docking.
• Classical QSAR Model Construction
• CoMFA model construction and result analysis
• CoMSIA model construction, method optimization and result analysis
• Compound structure modification through graphical result output

Our Capabilities

SYBYL is a professional tool for drug and molecular design with complete modules and powerful functions. It can be operated by a personal computer and is easy to use. The scientists of CD ComputaBio can provide novel inhibitor molecular design, 3D-QSAR modeling, molecular dynamics simulation, ADMET prediction.

Drug Design Services at CD ComputaBio

During drug design, our scientists screen out compounds that meet the Lipinski's rule of five. This type of compound has better pharmacokinetic properties, higher bioavailability during metabolism in vivo, and high draggability. Lipinski's rule of five:

• The relative molecular mass is less than 500
• The number of hydrogen bond donors is less than 5
• The number of hydrogen bond acceptors is less than 10
• The fat-water partition coefficient is less than 5
• The number of rotatable keys is less than 15

Features of SYBYL Software

• QSAR with CoMFA is a quantitative structure-activity relationship research tool set that can be used for structural modification and transformation of lead compounds.
• The extended functions of the advanced CoMFA module include several special molecular fields and QSAR extended tools.
• The VolSurf module predicts the absorption, distribution, metabolism, and excretion (ADME) properties of compounds.
• The GASP module uses a genetic algorithm for the prediction of receptor active sites.
• The Molconn-Z module is used to compute QSAR descriptors based on molecular topology.
• The FlexX module quickly and accurately performs flexible docking calculations between ligands and protein active sites for virtual screening.
• The GeneFold module predicts the structure and function of proteins by combining amino acid sequences with homology information and threading methods