1. Screening Libraries
  2. 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.


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 2 million purchasable compounds

•    3D pharmacophore model building

•    Consideration of water and solvation effects

Compound Databases

HY-L001V MCE Bioactive Compound Library 7,439 A unique collection of 7,439 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 8,383 Latest release of Ro3 Fragment Library comprising over 8,383 high-quality molecules. A useful tool for the fragment-based approach to drug discovery (FBDD).
HY-L0051V HTS Compound Library 1,938,649 Enamine HTS Collection contains 1,938,649 diverse screening compounds. These compounds frequently have unusual structures and unique properties. The collection is particularly recommended for the researchers looking for most diverse screening set.
HY-L0052V Advanced Library 531,580 Enamine Advanced Collection contains 531,580 compounds that have lead-like properties with MW ≤ 350, ClogP ≤ 3, and RotBonds ≤ 7 and/or valuable pharmacophores such carboxylic, primary amino and amide groups.
HY-L0053V Premium Library 138,801 Enamine Premium Collection contains over 138,801 compounds having most favorable molecular properties (high Fsp3, low logP and MW).
HY-L0072V Agro-like Library 15,085 Library of compounds intended for use in agro/crop science.
HY-L0059V Allosteric GPCR Library 17,385 A sub-library of Enamine’s GPCR Library designed for discovery of novel allosteric ligands.
HY-L0063V Allosteric Kinase Library 5,678 Carefully selected molecules via docking and visual evaluation.
HY-L0073V Antiviral Library 3,700 Nucleoside-like compounds able to act as antiviral.
HY-L0074V Aquaporins Library 1,500 A unique collection of 1,500 bioactive compounds targeting aquaporins.
HY-L0075V BACE Library 7,171 The library was designed to find molecules which target Beta-secretase (BACE).
HY-L0065V CNS Library 47,040 Library of novel small molecules with high CNS MPO scores.
HY-L0076V Covalent Screening Library 21,969 A set of screening compounds bearing “warheads” for covalent target modification.
HY-L0054V Discovery Diversity Set 10 10,240 Enamine Discovery Diversity Sets (DDS) are high-quality compound libraries focused on novel chemotypes and non-trivial structures. They compose of DDS-10 (10,240 compounds) and DDS-50 (50,240 compounds) sets which do not overlap. Discovery Diversity Set 10 contains 10,240 diverse screening compounds.
HY-L0055V Discovery Diversity Set 50 50,240 Enamine Discovery Diversity Sets (DDS) are high-quality compound libraries focused on novel chemotypes and non-trivial structures. They compose of DDS-10 (10,240 compounds) and DDS-50 (50,240 compounds) sets which do not overlap. Discovery Diversity Set 50 contains 50,240 diverse screening compounds.
HY-L0077V DNA Library 5,530 Designed for identification of new actives against proteins essential for DNA stability.
HY-L0078V Epigenetics Library 9,353 Library of compounds focusing to hit on a number of epigenetic targets.
HY-L0079V Glycomimetic Library 2,718 Specially synthesized set of compounds able to mimic glycosides and their interaction with proteins.
HY-L0058V GPCR Library 54,077 Designed for discovery of new GPCR ligands.
HY-L0056V Hit Locator Library 200 200,000 Enamine Hit Locator Library (HLL) is a sizable highly diverse screening set of 500,160 novel screening compounds. Hit Locator Library 200 (Core Set) contains 200,000 core compounds.
HY-L0057V Hit Locator Library 500 500,160 Enamine Hit Locator Library (HLL) is a sizable highly diverse screening set of 500,160 novel screening compounds. Hit Locator Library 500 (Entire Set) contains 500,160 compounds.
HY-L0070V IDO Targeted Library 5,502 IDO focused library designed by a combination of structure- and ligand-based methods.
HY-L0067V Immuno-Oncology Library 52,935 Designed for discovery of novel hits in Immuno-Oncology therapeutic area.
HY-L0064V Ion Channel Library 30,418 Designed for discovery of new Ion Channels ligands.
HY-L0071V JAK/STAT Compound Library 1,390 JAK/STAT Compound Library was designed to be a universal tool to search potential JAK-STAT pathway modulators.
HY-L0062V Kinase Hinge Region Directed Library 18,020 Kinase inhibitors targeting ATP binding pocket; designed using ligand-based methods.
HY-L0061V Kinase Library 67,385 Designed for discovery of novel protein kinase inhibitors.
HY-L0068V Kynurenine Pathway Library 12,300 The kynurenine pathway library is composed of 12,300 new potential active compounds for the kynurenine pathway.
HY-L0060V Lipid GPCR Library 7,512 A sub-library of Enamine’s GPCR Library designed for discovery of novel lipid GPCR ligands.
HY-L0080V Lipoxygenase Library 1,388 A set of LOXs inhibitors designed using docking and 2D similarity search.
HY-L0081V Molecular Chaperones Library 2,451 A set of compounds targeting molecular chaperones; designed by ligand-based methods.
HY-L0082V Nucleoside Mimetics Library 277 A set of Nucleoside Mimetics.
HY-L0083V Protein Mimetics Library 11,570 A set of 11,570 compounds targeting alpha-helix and beta-turn domains.
HY-L0066V Protein-Protein Interaction Library 59,370 Designed for discovery of novel PPI inhibitors.
HY-L0084V RNA Library 9,070 Library of compounds capable of binding to RNA.
HY-L0069V Serine Hydrolase Library 12,040 Library of precisely selected compounds able to form covalent bonds with catalytic serine residue.
HY-L0086V Specs HTS Compounds Library 210,454 Specs HTS library is a unique collection contains 210,454 diverse screening compounds for the lead identification via high-throughput screening (HTS) and high content screening (HCS).
HY-L0085V Tubulin Library 3,454 Library of potential tubulins ligands.

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 [email protected]