Molecular Docking Profacgen

The interactions between proteins and other molecules play important roles in various biological processes, including gene transcription and expression, metabolic regulation, signal transduction, and cell communication. Knowing structural aspects of a protein complexed with its binding partner can help understand the mechanism of such interaction and thus is important for drug discovery and development. However, it remains difficult and expensive to obtain complex structures by experimental methods, such as X-ray crystallography or NMR. Thus, computational docking is considered an important approach to predicting the three-dimensional structures of these interacting partners.

Profacgen employs computational docking techniques for a variety of purposes. Single docking experiments are useful for exploring protein functions, studying enzyme inhibitors and substrates, and elucidating biochemical pathways. Virtual screening of large databases of available chemicals can be applied for lead detection and optimization. The docking procedure also works seamlessly with upstream and downstream computational modeling protocols, which offers unparalleled opportunities for structure-based drug discovery.

Protein-Ligand Docking Profacgen employs docking techniques for a variety of purposes. Single docking experiments are useful for exploring the function of a protein, studying enzyme inhibitors and substrates, elucidating biochemical pathways. Most notably, docking can be applied to the virtual screening of large databases of available chemicals for lead detection and optimization, which offers unparalleled opportunities for structure-based drug design and discovery.

Protein–Lipid Docking Profacgen makes use of the state-of-the-art computational software tools to predict these protein–lipid interactions. The lipid binding sites of a protein can be deduced from its amino acid sequence, and/or predicted from its three- dimensional structure using molecular docking protocols. Our docking method combines sequence and structure information, and explores the most energetically favorable protein-lipid complex. The scoring function is specifically designed to allow for the prediction of lipid distortion and protein conformational changes associated with the binding event. Experiment-derived restraints can also be applied to limit the search space. The structures with best values of binding energies are clustered and representatives of the largest clusters are selected for structural optimization by energy minimization before being presented to the customer. The stability of docked complexes can be further tested through molecular dynamic simulations.

Antibody-Antigen Docking Profacgen employs computational docking techniques to search all possible binding modes in the translational and rotational space between an antibody (Fv, Fab, or full antibody) and its antigen, with modeling of conformational changes of the variable loops upon complex formation. This is an important means for understanding the physicochemical forces that underlie macromolecular interactions, and a working hypothesis can be build based on the docked complex, guiding further experiments for the rational design of antibody-based therapeutics.

Protein-Peptide Docking Profacgen employs computational docking techniques to search all possible binding modes in the translational and rotational space between a protein receptor and its peptide binding partner. Given a protein receptor structure and a peptide sequence, we predict the structure of protein–peptide complex, starting from random conformations and positions of the peptide. This is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modeling protein–peptide complex structures at the atomic level. Furthermore, the precise understanding of these interactions will facilitate the rational design of potentially therapeutic peptide.

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