Virtual Screening (VS) is a screening of active compounds based on small molecule databases. Ligand-based virtual screening (LBVS) is one of the two major types of computing techniques for virtual screening. The LBVS method attempts to prioritize candidate molecules instead of determining whether the candidate molecules are active. Usually, a simple LBVS process includes only a few steps. First, establish a molecular representation of each input molecule. Second, the similarity between candidate molecules and known active molecules will be evaluated and ranked according to their respective scores. Finally, a small number of active compounds will be identified from a library containing a large number of inactive compounds.

Figure 1. Process of ligand-based virtual screening (LBVS).

Overall solutions

• Pharmacophore modeling

Pharmacophore modeling is to study the pharmacophore of a series of known active compounds, and summarize some groups that play a key role in the activity of the compound through conformational analysis, molecular superposition and other methods Information.

• Quantitative structure activity relationship (QSAR)

QSAR quantitatively studies the interaction between small organic molecules and biological macromolecules by means of mathematical and statistical methods with the help of the physical and chemical properties of molecules or structural parameters. It can be used to determine the absorption, distribution, metabolism, excretion, and other physiologically related properties in the organism.

• Structual similarity, SSIM

SSIM is to perform similarity matching through various descriptors or fingerprints to determine whether the compound has similar activity or therapeutic mechanism.

Our services

The LBVS services provided by CD ComputaBio are listed as below, which including but not limited to:

• Small Molecule Alignment
• Descriptor Based Screening (both 2D and 3D)
• Pharmacophore Similarity Search
• Recursive Partitioning
• Graph-Based Similarity Assessment

Our advantages

• Fast screening speed, good versatility (not limited by target structure).
• Comprehensive consideration including both water and solvation effects.
• Super high-performance computer.
• Compound database compliant with predefined filtering rules.

CD ComputaBio can offer you but not limited to:

• Structure-based Virtual Screening (SBVS) Service
• Reverse Virtual Screening
• 3D-QSAR Service

CD ComputaBio' ligand-based virtual screening service can significantly reduce the cost and labor of the subsequent experiments. Virtual screening technology service is a personalized and customized innovative scientific research service. Each project needs to be evaluated before the corresponding analysis plan and price can be determined. If you want to know more about service prices or technical details, please feel free to contact us.

Ligand-based Virtual Screening (LBVS) FAQS

• • Q: What are the priorities for ligand-based virtual screening?

    • A: Ligand-based virtual screening (LBVS) is one of the two main classes of virtual screening computational techniques. Based on the fact that ligands similar to the active ligand are more likely to be active than random ligands, LBVS methods attempt to prioritize candidate molecules rather than deciding whether the candidate molecule is active or not. Typically, a simple LBVS process consists of only a few steps. First, a molecular representation of each input molecule is constructed. Next, similarities between the candidate molecules and known active molecules will be evaluated and ranked. In the next step, the candidates will be ranked according to their respective scores. Finally, a small number of active compounds will be identified from a library containing a large number of inactive compounds.

  • Q: How long do ligand-based methods take?

    • A: Ligand-based methods typically require a fraction of a second to complete a single structure comparison operation. Sometimes a single CPU is sufficient to perform a large screen in a few hours. However, multiple comparisons can abe performed in parallel to speed up the processing of large compound databases.

  • Q: How accurate is the ligand-based virtual screening?

    • A: The goal of the virtual screening is to identify molecules with novel chemical structures that bind to the macromolecular target of interest. Thus, the success of a virtual screen is defined by finding interesting new scaffolds rather than by the total number of hits. Therefore, the interpretation of the accuracy of the virtual screen should be considered with caution. The low hit rate of interesting scaffolds is clearly superior to the high hit rate of known scaffolds. In contrast, in the intended application of virtual screening, the resulting hits are subject to experimental confirmation (e.g., IC₅₀ measurements). It is agreed that retrospective benchmarks are not good predictors of prospective performance, and therefore only prospective studies can constitute conclusive evidence of the applicability of a technique to a specific target.

  • Q: What are the various LBVS methods?

    • A: The methods we can offer include 2D molecular similarity methods (fingerprint-based methods), 3D similarity searches (physicochemical properties of molecular shapes colored or uncolored, pharmacophore and energy fields around the molecule such as electrostatic properties), machine learning and 2D/3D QSAR (quantitative structure-activity properties) modeling.

  • Q: Can pharmacophore modeling be used for LBVS?

    • A: Pharmacophore modeling has been used extensively in LBVS to generate predictive models suitable for novel compound design. CD ComputaBio constructs pharmacophore models by overlaying a set of structurally diverse compounds that bind to the same target and extracting common chemical features that are critical to their biological activity. Potential ligand candidates can be identified by using the pharmacophore model to virtually screen a library of compounds.

  • Q: What is the Principles of Ligand-Based Virtual Screening (LBVS)?

    • A: The principle behind LBVS is based on the assumption that structurally similar compounds have similar biological activity. Therefore, the screening process involves comparing the chemical structures of known active compounds against a database of compounds to identify those with similar structures. The selected compounds are then further refined through a series of computational simulations until a suitable candidate is identified.

  • Q: What algorithms are used in the Ligand-Based Virtual Screening (LBVS) ?

    • A: There are two main algorithms used in LBVS: similarity-based and pharmacophore-based screening. Similarity-based screening involves searching a database of compounds for those that are structurally similar to known active compounds. Pharmacophore-based screening, on the other hand, involves identifying key features of known active compounds, such as functional groups or atoms, and searching for compounds with similar features.

  • Q: What software are available for LBVS calculations?

    • A: There are several software programs available for LBVS calculations, such as OpenEye, Schrodinger, and BIOVIA. These programs use different algorithms and approaches to LBVS calculations, and the choice of software will depend on the specific requirements of the screening process.

  • Q: What are the process of LBVS calculations?

    • A: The LBVS process involves several steps, including data preparation, feature identification, similarity or pharmacophore search, molecular docking, and hit selection. In the data preparation stage, compounds are selected and preprocessed by removing duplicates, standardizing their formats, and assigning molecular properties. In the feature identification stage, known active compounds are analyzed to identify key structural features, such as functional groups or atoms. In the similarity or pharmacophore search stage, a database of compounds is searched for those that share similar features with the known active compounds. In the molecular docking stage, the selected compounds are docked into the binding site of the target protein to assess their binding affinity. Finally, in the hit selection stage, compounds with high binding affinity are selected for further analysis and experimental validation.

  • Q: What are the advantages of LBVS calculations?

    • A: Pharmacophore modeling has been used extensively in LBVS to generate predictive models suitable for novel compound design. CD ComputaBio constructs pharmacophore models by overlaying a set of structurally diverse compounds that bind to the same target and extracting common chemical features that are critical to their biological activity. Potential ligand candidates can be identified by using the pharmacophore model to virtually screen a library of compounds.