Surflex-Dock is a molecular docking module in SYBYL software, which uses a unique empirical scoring function and a search engine based on molecular similarity to dock ligand molecules to protein binding sites. Surflex-Dock uses the protomol to represent the binding pocket of the protein, and uses probes to probe the surface hydrophobicity, hydrogen bonding and electrostatic properties of the protein pocket to generate a negative image of the protein's active pocket. Surflex-Dock introduces four molecular docking modes: Surflex-Dock Normal, Surflex-Dock Screen, Surflex-Dock Geom, and Surflex-Dock GenomX, which can realize flexible protein docking, restricted docking, DNA-targeted docking and other special docking modes. We use Surflex-Dock software to study the binding mode and interaction between small molecule ligands and macromolecular proteins, and predict or explain the activity of molecules.
The purpose of molecular docking is to find the optimal binding mode of ligand molecules and receptor molecules. Therefore, with the support of Surflex-Dock software, our team strives to solve the most important problems facing molecular docking to find the best binding site and evaluate the binding strength between docked molecules.
Our method relies entirely on structure-generated force fields, is accurate for typical drug-like ligands, and has better coverage of different conformations, but is not suitable for known structural libraries.
Our approach is based on a fundamentally different representation of molecular shape. We take the molecular surface directly comparing coulomb electrostatic fields, and we model hydrogen bonding in a direction-sensitive manner.
Our method is fully automated in aligning and selecting appropriate binding site variants. Powerful use of fully automatic modes is for virtual screening and pose prediction.
Affinity prediction is an extremely challenging field, especially when the target structure is unknown. Our research employs machine learning (not directly physics-based simulations) to accomplish the following subtasks:
At CD ComputaBio, what we can simulate with the support of Surflex-Dock software includes modeling of small drug molecules, conformational analysis, 3D quantitative structure-activity relationship studies, pharmacophore modeling, virtual screening, and homology of biological macromolecules modeling, active site analysis, database searches,etc.