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

By: Biomoltech  09-12-2011
Keywords: Competitive Programs, Docking Software

Lead Finder's Main Application Areas

Docking of small molecules to protein structures and evaluation of parameters of such molecular interaction is relevant to studies in many life science areas. However, virtual screening, ligand docking and estimation of binding energy of protein-ligand interaction are clearly the three primary application areas for Lead Finder. Additionally, Lead Finder can be used to prepare protein structures for independent docking experiments.

  • Lead Finder correctly predicts 3D structure of non-covalently and covalently bound protein-ligand complexes in most cases. 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. Our test set was a combination of test sets of such molecular docking software as , , , , , . With this test set, we attempted a straightforward comparison of Lead Finder's performance to that of competitive programs. As shown in our , Lead Finder has outperformed all competitive programs on their native test sets.

Keywords: Competitive Programs, Docking Software

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Pre-docking Preparation of Protein Structures

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 model. SCP theory treats microenvironment-dependent energy of electrostatic interactions as a function of local hydrophilicity and degree of solvent exposure.


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.