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Structure-Based Virtual Screening Service

Overview

Table 1. Estimated Price and Lead time for Structure-Based Virtual Screening

Chemicals Estimated Price(In USD) Lead-time
500,000 1,000 1 week
1,000,000 1,500
2,000,000 2,000
3,000,000 2,300 2 weeks
4,000,000 2,500

Currently, we have more than 4.8 million chemicals in our database ready for virtual screening. These chemicals includes AsisChem(2233602 chemicals), Mcule(2196827 chemicals), Molport(1946265 chemicals), Enamine(1040264 chemicals), UORSY(846282 chemicals), ChemBridge(673573 chemicals), Asinex(604337 chemicals), TimTec(565237 chemicals), Vitas-M(366693 chemicals), ChemDiv(256790 chemicals), IBScreen(156887 chemicals), Life Chemicals(121196 chemicals), Zelinsky Institute(114161 chemicals), Specs(85207 chemicals), Maybridge(10199 chemicals), DrugBank(2959 chemicals) and so on.

Deliverables

Deliverables

  1. Virtual Screening Report: target protein model preparation; docking box selection; docking and analysis of results.
  2. TOP 1000 models.
  3. TOP 10 model analyses.

Lead Time: 1-2 weeks.

How to start?

At NovoPro, you only need to provide biological information associated with the target, and we can perform SBVS. Through this process, we can screen out a series of hits and corresponding binding modes. Biological assays can be provided to determine the activity of compounds obtained through SBVS.

To estimate the screening price, simply select the appropriate parameters below for your project and click the 'Query Database' button. It will return the size of the database you specify and the estimated price. To place the order, you may also need to send us your selection of these parameters.

Total: 3513333 chemicals, estimated price for VS:2406 USD

Background

Structure-based virtual screening (SBVS), also known as target-based virtual screening (TBVS), attempts to predict the best interaction between ligands against a molecular target to form a complex. As a result, the ligands are ranked according to their affinity to the target, and the most promising compounds are shown at the top of the list. SBVS methods require that the 3D structure of the target protein be known so that the interactions between the target and each chemical compound can be predicted in silico. Among the techniques of SBVS, molecular docking is noteworthy due to its low computational cost and good results achieved.

The use of SBVS has advantages and disadvantages. Among the advantages are the following:

  1. There is a decrease in the time and cost involved in the screening of millions of small molecules.
  2. There is no need for the physical existence of the molecule, so it can be tested computationally even before being synthesized.
  3. There are several tools available to assist SBVS.

The disadvantages can be highlighted as the following:

  1. Some tools work best in specific cases, but not in more general cases (Lionta et al., 2014).
  2. It is difficult to accurately predict the correct binding position and classification of compounds due to the difficulty of parameterizing the complexity of ligand-receptor binding interactions.
  3. It can generate false positives and false negatives.

SBVS strategies usually rely on the following procedures: (1) Target selection and preparation, (2) compound database selection, (3) molecular docking, and (4) analysis of results. Obtaining the target 3D structure is the starting point of the SBVS project. We can search for the PDB database (https://www.rcsb.org/) to find the structure that has been determined or obtain the target structure through modeling. In addition, we can utilize mainstream structural biology technologies, including X-ray crystallography and cryo-electron microscopy (cryo-EM) to provide a one-stop target structure analysis solution from gene to structure. With the aid of computational analysis, we investigate the protein surface from multiple perspectives such as topology, physicochemical properties, and force field to predict the appropriate binding site.

The second important issue is to select and prepare a suitable compound library. NovoPro can perform large-scale SBVS against multiple public and commercial chemical databases and has created in-house databases on the drug-like properties of different chemical species. Moreover, we can also customize the library preparation according to your project requirements.