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Structure-based Virtual Screening


Structure-based virtual screening (SBVS), also known as target-based virtual screening (TBVS), is used to predict the interaction between ligands against a molecular target to form a complex. In the SBVS process, the ligands are ranked according to their affinity to the target, and the most promising compounds are presented at the top of the list. The target protein with 3D structure is required for the in silico prediction of the interactions between the target and each chemical compound.

Advantages of SBVS

  • Reduce the time and cost involved in the screening of millions of small molecules.
  • Perform computationally before molecule being synthesized.
  • Multiple computational tools available to assist SBVS.

Overview of the typical workflow of structure-based virtual screening (SBVS).Figure 1. Overview of the typical workflow of structure-based virtual screening (SBVS). (Shaherin, B.; et al. 2018)

SBVS Process

Alfa Chemistry has developed SBVS strategies that rely on the following procedures:

  • Protein preparation

We select and prepare the protein that are closely related to a particular disease.

  • Binding site identification

Our teams use three methods for the binding site identification:

1. Static approach: Computational solvent mapping with chemical probes is applied.
2. Dynamic approach: The probes and the protein evolve dynamically in time.
3. Mixed approach: A chemical probe is used as in the static approach and in addition, the putative binding site is evaluated in terms of flexibility.

  • Compound database preparation

We design and synthesize a library of compounds containing a variety of small-molecule fragments of drugs. The mall molecule fragment has a certain affinity for the active site of the target, such as the target protein or the targeting enzyme.

  • Docking and scoring

We perform screening of small synthesized fragments using pre-designed targets using various methods such as molecular docking.

  • Results analysis

According to the results of the screening, molecular fragments with better activity can be obtained, and the lead compounds can also be obtained by appropriately combining the fragments.

  • Modification and optimization

The chemical structure of the obtained lead compound is further modified and optimized to obtain a drug candidate for clinical research.

Our LBVS Services

  • Molecular docking

Our scientists apply molecular docking approach in structure-based design to screen a library of compounds to identify compounds with a higher affinity toward their target protein by elucidating their mode of interaction with their target utilizing their 3D structures. We can confirm their bioavailability via their pharmacokinetics and drug-likeness properties.

  • Ensemble docking (ED)

We use the conformational system in ensemble docking to comprehensively characterize the receptor binding site, in which docking each ligand with multiple rigid conformations of the receptor is performed. Our experts apply ensemble docking method to explore a broader chemical space.

  • Consensus Induced-Fit Docking (cIFD)

CIFD method allows the protein binding site to adapt to multiple ligands during SBVS. Alfa Chemistry applies this method in some challenging docking programs since it can improve the probability of identifying accurately docked poses.

  • Molecular dynamics (MD) simulation

We perform MD simulation and QMMM calculations to further investigate the high ranked compounds and deliver a structure with a stronger interaction with target's active site, which could be a favorable candidacy for biological assessment and additional advanced improvement.

  • Scoring functions

We mainly apply force field-based function, empirical scoring functions and knowledge-based functions to estimate the free energy of binding of a ligand to a specific target based on a generated docked pose after docking different ligands of a database.

Application of Our SBVS Services

  • Investigate the pathways of interactions (e.g. kinetic of binding, unbinding event)
  • Explore binding pockets and/or discover cryptic pockets
  • Affinity prediction

Alfa Chemistry's Advantages

  • Alfa Chemistry enables researchers to apply LBVS utilizing various chemical libraries on traditional or more challenging protein targets such as protein-protein interactions.
  • We are capable of performing docking into a user-defined binding site or blind docking using our automated LBVS methods.
  • We provide state-of-the-art SBVS techniques and software tools to support molecular docking, molecular dynamics simulations and free energy calculations.

Our structure-based virtual screening services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Shaherin, B.; et al. Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design. Frontiers in Pharmacology. 2018, 9:128.

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