Pre-docking Preparation of Protein Structures

By: Biomoltech  09-12-2011

Lead Finder uses an original theoretical approach to assign optimal ionization states of protein residues at arbitrary pH conditions, which is based on the recently introduced screened coulomb potential (SCP) model

. SCP theory treats microenvironment-dependent energy of electrostatic interactions as a function of local hydrophilicity and degree of solvent exposure. Details of the SCP model implementation in Lead Finder can be found in the


Other products and services from Biomoltech


Lead Finder - a software solution for virtual screening and molecular docking

Accuracy of protein-ligand docking has been validated on a set of 407 protein-ligand complexes, which appears to be the most extensive benchmarking study of such kind at present. However, virtual screening, ligand docking and estimation of binding energy of protein-ligand interaction are clearly the three primary application areas for Lead Finder.


Prediction of 3D structure of protein-ligand complexes

While many configuration options are available to end users to fine-tune docking calculations, two calculation regimes, docking and screening, have been created to provide the optimum balance between the speed of calculations and the accuracy of predictions.


Estimation of Free Energy of Binding in Protein-Ligand Complexes

This functionality is novel to docking software since binding energy calculation is usually done in separate software packages that are based on various theoretical approaches including free energy perturbation, linear interaction energy, etc.


Virtual Screening of Libraries of Chemical Compounds

To accelerate processing of large libraries in virtual screening experiments, Lead Finder employs a special modification of the docking algorithm called screening mode. During virtual screening each ligand from a library is docked to a target protein, and ligands are rank-ordered according to their binding potencies.