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Molecular Modeling and Lead Discovery

Molecular Modeling and Lead DiscoveryStarting with the rationally selected molecules improves the probability of finding a hit. We provide high quality, efficient and cost-effective integrated computational drug discovery services and will design any target-specific set of compounds for your screening program with the aid of state-of-the-art molecular modeling and computational chemistry methods. Structural optimization and synthetic chemistry support is also available

Our company has a strong track-record in organic chemistry, molecular biology and molecular modeling. Please see the list of our publications. At our disposal is a stock collection of about 260,000 Screening Compounds immediately available for screening. 75 % of compounds from the collection satisfy Lipinski's Rule of Five and 50 % match lead-like criteria. Using this collection we developed more than 10 classes of novel and potent inhibitors of protein kinases CK2, ASK1, FGFR1, polymerases PARP-1, HCV NS5B and leucyl-tRNA synthetase.



The variety of our services includes:
  • Rational design of small organic ligands against biological target of interest within efficient infrastructure of molecular modeling, biochemical screening and organic synthesis facilities.
  • Computational chemistry services (drug-likeness prediction, diversity calculations, compound filtering by any physico-chemical properties)
  • Pharmacophore search and scaffold hopping
  • Preparation of custom target-focused libraries
  • Receptor-based virtual screening and design (molecular docking)
  • Ligand-based activity prediction (QSAR)
  • Target structure comparative modeling
  • Hit-to-lead optimization (improvement of compounds' activity, selectivity and ADME properties)
  • Molecular dynamics simulation of macromolecules and their complexes with small molecule ligands


Our company has over 15 years of experience in molecular modeling/hit-to-lead optimization.  We guarantee quality, competitive pricing, and a fast turn-around time. We already collaborate with many companies and academic institutions in Europe, the US and Canada, and we hope you will consider working with us.



  • Creativity and chemistry/biology problem solving
  • Weekly progress reports
  • Competitive pricing and fast turn-around time
  • Reliability, strict confidentiality and intellectual property (IP) protection guarantee
  • Prompt response policy
  • FTE (Full Time Equivalent) FFS (Fee For Services) projects
  • Respond to inquiries within 24 hours
  • Molecular modeling and computational chemistry procedures with modern state-of-the-art software and algorithms


Our experts have implemented a number of crucial improvements to a calculation algorithm, which includes calculation of atom charges as well as unique force field and scoring functions. 
Taking into account key electrostatic interactions between molecules, we developed a specific charge-definition algorithm which uses Kirchhoff method for electronegativity relaxation. This allowed us to calculate electrostatic terms more accurately. To achieve reasonable acceleration in entropy loss measurement, we applied harmonic approximation for integration of configuration space of a ligand-receptor complex.  Scoring function also requires co-crystallized water environment to be efficient, therefore, we developed new method to calculate and predict binding of water molecules to the formed complex on sub-second timescale. 
Our approach to Receptor-Based virtual screening includes drug-likeness filtering, molecular docking, 3D-pharmacophore search, re-scoring, key intermolecular hydrogen bond detection and visual inspection of ligand-receptor complexes. A panel of our experts analyzes the compound complexes generated by virtual screening manually and look into the diversity of chemical scaffolds.  
They visually inspect ligand-receptor complexes for proper binding mode: hydrogen bonding, hydrophobic interactions as well as orientation of the ligand in binding site. Therefore, each compound is finally selected manually which allows high accuracy in the selection. It is demanding, but in this way we could insure that our customers will get the most promising molecule candidates for their specific tasks. Our approach has been proven to work and our scientists have already found a number of new kinase inhibitors with high activity and selectivity. 
The approach used to Ligand-Based compound screening is based on the suggestion that Activity = function of a Structure. It compares structures of new compounds with structures of well-known biologically active substances (“training set”). The training set we use consists of about 200,000 of biologically active compounds. They include already launched drugs, drug-candidates under clinical or advanced preclinical tests, leads and toxic compounds. Together, they cover about 4,500 kinds of biological activities including basic pharmacological effects, action mechanisms and specific toxicities.
Also, please check the list of our target-focused libraries designed with our virtual screening approaches.


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