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  2. Screening Libraries
  3. Virtual Screening

Virtual Screening


In the last decades, high-throughput screening (HTS), which refers the experimental screening of large libraries of chemicals against a biological target, plays a crucial role in the identification of new lead compounds in the early-stage drug discovery. However, HTS requires expensive equipment and facilities, and its success depends on the size of the compound library. The high cost and low hit rate associated with HTS have stimulated the development of in silico virtual screening (VS). Virtual screening is a computational technique used to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target. Nowadays, it has become a crucial step in early-stage drug discovery owing to its unique advantages over experimental HTS: drug target-relevant, competitive price and efficient.

MedChemExpress (MCE) provides high quality virtual screening service that enables researchers to identify most promising candidates. Based on the laws of quantum and molecular physics, our virtual screening services can achieve highly accurate results. Our optimized virtual screening protocol can reduce the size of chemical library to be screened experimentally, increase the likelihood to find innovative hits in a faster and less expensive manner, and mitigate the risk of failure in the lead optimization process.

Virtual Screening


The virtual screening methods are mainly divided into two types: structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS).

•   SBVS

The general scheme of a SBVS strategy starts with processing the 3D target structural information of pharmaceutical protein interested (determined either experimentally or computationally through homology modeling) and then dock the small molecules to targeted binding sites. These docked compounds are then ranked based on their predicted binding affinity or complementarity to the binding site, as well as other criteria. Usually only a few top-ranked compounds are selected as candidates for further experimental assays. Our fast and accurate ligand docking and scoring procedures lead to efficient virtual screening.

•   LBVS

In the absence of 3D structures of potential drug targets, LBVS is one of the most popular approaches for drug discovery and lead optimization. Biological data are explored in order to identify known active or inactive compounds that will be used to retrieve other potentially active molecular scaffolds for experimental evaluation. LBVS methods include approaches such as similarity and substructure searching, quantitative structure-activity relationships (QSAR), pharmacophore mapping, and machine learning.

Screening Process

•    Target research

•    Model building

•    Preparation of small molecule compound library

•    Molecular docking/pharmacophore mapping

•    Scoring/ranking

•    Compound selection


•    Ligand-based and structure-based virtual screening

•    Super high-performance computer

•    Compound database containing over 16 million purchasable compounds

•    3D pharmacophore model building

•    Consideration of water and solvation effects

MCE SBVS Protocol

Compound Databases

Cat. No. Name Size Description
HY-L001V MCE Bioactive Compound Library 22,275 A unique collection of 23,000 bioactive and structurally diverse compounds. Bioactivity and safety confirmed by preclinical research and clinical trials. Some have been approved by FDA.
HY-L032V MCE Fragment Library 22,464 Latest release of Ro3 Fragment Library comprising over 22,464 high-quality molecules. A useful tool for the fragment-based approach to drug discovery (FBDD).
HY-L0113V 1M Drug Fragment-Based Diversity Library 1,000,000 A diversity compound library contains 1,000,000 compounds with at least one drug fragment. Drug fragments are derived from 2946 FDA-approved drugs by BRICS and Recap algorithm. It is suitable for AI drug screening, virtual screening, discovery of lead compounds.
HY-L0120V Asinex BioDesign Library 170,269 Asinex use “BioDesign” approach to design this collection. “BioDesign” approach incorporates key structural features of known pharmacologically relevant natural products (e.g. alkaloids and other secondary metabolites) into synthetically feasible medicinal chemistry scaffolds.
HY-L0118V Asinex Covalent Inhibitors Library 8,085 A unique set of molecules containing mild electrophilic moieties that covalently interact with amino acid residues in the target protein.
HY-L0117V Asinex Macrocycles for Glycomimetics Library 1,412 Macrocyclic glycomimetics are an extremely interesting class of glycomimetics as they occupy space between small and macro molecules. Macrocyclic glycomimetics are mostly represented by naturally occurring molecules derived from marine microorganisms and bacterial or fungal metabolites.
HY-L0116V Asinex Macrocycles for RNA Library 1,065 The library consists of very diverse, drug-like molecules which incorporate certain known RNA-recognition elements distributed within macrocyclic rings or peripheral fragments.
HY-L0115V Asinex Macrocycles Library 10,091 Asinex has elaborated a library of diverse macrocycles using an effective tool box of synthetic methods. The resulting scaffolds are novel and tremendously diverse, medchem-relevant, macrocyclic frameworks.
HY-L0119V Asinex PPI Pre-Plated Library 3,253 The PPI Library comprises molecules of various sizes, frameworks, and shapes ranging from fragment-like entities to macrocyclic derivatives designed as secondary structure mimetics or as epitope mimetics.
HY-L0091V Chemspace Lead-Like Compound Library 981,244
HY-L0093V Chemspace Scaffold derived set 10,119 Composed of 10,119 compounds, which including 3,373 scaffolds, 3 compounds per each.
HY-L0094V Chinese National Compound Library 1,398,968 1.4 million compounds possessing diversified structures.
HY-L0101V FCH Group Screening Library 2,244,487 FCH Group Screening Library contains about 2,244,487 lead-like compounds for biological screening.
HY-L0105V InterBioScreen Synthetic Compounds Library 485,000 InterBioScreen Synthetic Compounds Library contains about 485,000 immediately available compounds.
HY-L0088V Life Chemicals 50K Diversity Library 50,240
HY-L0087V Life Chemicals HTS Compound Collection 494,471 Life Chemicals HTS library is a unique collection contains 494 diverse screening compounds for the lead identification via high-throughput screening (HTS) and high content screening (HCS).
HY-L0107V Life Chemicals Natural Product-like Compound Library 13,236 This library contains 13,236 in-stock natural product-like compounds. Designed by 2D fingerprint similarity filtering, chemical descriptor-based and natural-likeness scoring selection.
HY-L0121V MCE 10K Natural Product-like Compound Library 10,000 This Library consists of 10,000 natural product-like compounds. Each compound has scaffold of natural products or Tanimoto coefficient >0.6 with natural products. The natural-likeness scoring of these compounds is >-2. What’s more, compounds in the library are drug-like and readily available for re-supply, making it a powerful tool for new drug research and development.
HY-L912V MegaUni 10M Virtual Diversity Library 10,000,000 A unique collection contains 10,000,000 synthetically accessible screening compounds for the novel lead identification. Easy to synthesize via standard 1-2 step procedures.
HY-L910V MegaUni 50K Virtual Diversity Library 50,000 A novel collection of synthetically accessible, lead-like compounds of exceptional structural diversity. Easy to synthesize via standard 1-2 step procedures.
HY-L0095V OTAVAchemicals Screening Collection 270,000 OTAVAchemicals Screening Collection contains about 270,000 re-supply compounds for prompt delivery.
HY-L0114V Pharmeks Screening Compound Library 439,804 This library contains about 439,804 natural and synthetic screening compounds.
HY-L0106V Protein-Protein Interaction Modulators Library 2,906 Designed for discovery of PPI modulators.
HY-L0086V Specs HTS Compounds Library 208,670 Specs HTS library is a unique collection contains 208 diverse screening compounds for the lead identification via high-throughput screening (HTS) and high content screening (HCS).
HY-L0104V UORSY New Generation Screening Library 1,900,000 UORSY New Generation Screening Library contains about 1,900,000 compounds. The library is a revolutionary collection of lead-like molecules with outstanding structural quality and diversity—New Generation Screening Library (NGSL).
HY-L0103V UORSY Screening Library 680,000 UORSY Screening Library contains about 680,000 compounds. The library has extensively developed a polymerization synthesis method that provides a highly diverse chemical structure.
HY-L0096V Vitas-M Screening Compounds Library 1,400,000 Stock of synthetic small molecule organic compounds for biological screening and lead optimization. It is the best source to make "cherry pick" selection as per your criteria.

MedChemExpress (MCE) virtual screening services can significantly improve the hit rates and reduce the costs of compound screening. If you have any questions, please do not hesitate to contact us via email sales@MedChemExpress.com.

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