Applications of UCSF DOCK Software

The UCSF DOCK program was created in the 1980s by Irwin "Tack" Kuntz's group as the first docking program. UCSF DOCK uses geometric algorithms to predict the binding mode of small molecules. Brian K. Shoichet, David A. Case, and Robert C. Rizzo are co-developers of DOCK. Two versions of the docking program are under active development: DOCK 6 and DOCK 3. The UCSF DOCK algorithm uses a geometric matching algorithm to superimpose ligands onto the negative image of the binding pocket to solve rigid body docking problems. Important features have been added to improve the algorithm's ability to find the lowest energy binding mode, including force field-based scoring, dynamic optimization, an improved rigid body docking matching algorithm, and a flexible ligand docking algorithm. The docking methods are rigid docking: shape matching, using spheres placed in pockets and performing bipartite matching between these spheres and molecules (all versions). Flexible ligands are described using an algorithm called anchor and grow (v4-v6), and hierarchical docking of databases.

Our Services Based on UCSF DOCK Software

On the UCSF DOCK software platform, CD ComputaBio can provide customers with high-quality computational biology services.

• Orientation Search
  UCSF DOCK has a new direction search algorithm, or matching algorithm. At CD ComputaBio, our scientists can control the number of orientation samples in two ways: automatic matching and manual matching based on UCSF DOCK software.
• Conformation Search
  Flexible molecules are viewed as collections of rigid fragments. The first step in segmentation is ring identification. All bonds within a molecular ring are considered rigid bonds.
• Database Processing
  Our scientists use DOCK to process molecular databases to find potential inhibitors or ligands for target macromolecules.
• Site Characterization
  The macromolecular structures you are working with may include ligands, and crystal structures often contain water molecules and sometimes ions found on the surface of proteins. At CD ComputaBio, our scientists create molecular surfaces on UCSF DOCK Software, remove ligands and water of crystallization, and characterize active sites on macromolecular proteins.
• Macromolecular Docking
  The protein-protein docking problem is one of the research hotspots in computational biophysics and structural biology. Our scientists use known protein structures together with computational methods such as experimental methods or models of homologous proteins, especially in the context of structural genomics.
• Structure-based Drug Design (SBDD)
  Our computational and medicinal chemists routinely apply SBDD to guide the iterative design of compounds. The size, shape, and charge of drug molecules are expected to be taken into account to improve interactions with target proteins and to find regions where molecular and physical properties can be modulated without compromising drug-protein interactions.

Our Capabilities

CD ComputaBio has successfully used the UCSF DOCK to identify centralized screening sets with high hit rates in bioassays. We have >90% hit discovery success for multiple targets including kinases, protein-protein interactions, ion channels, and proteases. Our medicinal chemists have successfully advanced many of these projects to the drug candidate stage.

The Features of UCSF DOCK Software

• No need to physically screen 1000,000 compounds. Typically, only about 7000 compounds are screened to identify hits.
• It's fast! Identifying confirmed detection hits takes only a few weeks.
• It was a success: we had >90% success in finding detection hits across object classes.
• Flexible ligands are described using an algorithm called anchor and grow and hierarchical docking of databases.
• UCSF DOCK software is designed specifically for macromolecular docking software.