Can you screen custom compound libraries?

Yes, we routinely screen client-provided proprietary libraries. We support all standard chemical formats, including SDF, Mol2, and SMILES. Our preprocessing pipeline includes ligand state preparation (pH 7. ± 2.), tautomer enumeration, and high-quality 3D conformation generation. We also provide access to massive 'make-on-demand' catalogs from top vendors like Enamine and Mcule.

Virtual Screening Services for Drug Discovery

- Screen custom, commercial, natural product, fragment, or approved-drug libraries
- Support targets with crystal structures, AlphaFold models, homology models, or known ligands
- Deliver ranked, interpretable hit lists for downstream biochemical or cellular validation

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# Virtual Screening # Hit Identification # In Silico Screening # Structure-Based Design # Ligand-Based Design # High-Throughput Screening # GPCR # Kinase Inhibitors # Molecular Docking # Pharmacophore Modeling # Virtual Screening # Hit Identification # In Silico Screening # Structure-Based Design # Ligand-Based Design # High-Throughput Screening # GPCR # Kinase Inhibitors # Molecular Docking # Pharmacophore Modeling

When Do You Need Virtual Screening?

Virtual screening is not only a computational method; it is a practical decision-support workflow for narrowing chemical space, prioritizing testable candidates, and reducing early-stage discovery risk.

In drug discovery, virtual screening uses computational workflows to evaluate compounds against a target, known ligand profile, pharmacophore model, or disease-related screening objective. Instead of only describing the method, the scenarios below show when clients usually need virtual screening and what CD ComputaBio can deliver for each project situation.

You may benefit from virtual screening if you:

have a validated target but no starting compounds;
have a compound library but need prioritization before testing;
want to identify drug repurposing candidates;
need to explore new scaffolds beyond known analogs;
want to reduce the cost of experimental HTS;
need computational support before medicinal chemistry optimization.

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Areas of Expertise

Applications of Virtual Screening Services

Our computational screening solutions cover a wide range of therapeutic targets and discovery scenarios.

Virtual Screening For Kinase Inhibitors

Targeting signaling pathways.

Screening for ATP-competitive inhibitors.
Allosteric modulator identification.
Selectivity profiling against kinase panels.

Virtual Screening ForGPCR Drug Discovery

Addressing complex membrane proteins.

Homology modeling for targets without crystal structures.
Ligand-based screening for orphan GPCRs.
Bias signaling pathway analysis.

Virtual Screening For PPI Inhibitors

Protein-Protein Interaction modulation.

Targeting large, flat binding interfaces.
Peptide and peptidomimetic screening.
Fragment-based screening for hot-spot targeting.

Virtual Screening For Antiviral Drug Discovery

Combatting infectious diseases.

Screening against viral proteases and polymerases.
Drug repurposing libraries for rapid response.
Nucleoside analog screening.

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Our Virtual Screening Solutions

Target-focused computational strategies designed to address specific drug discovery challenges.

Small Molecule Drug Virtual Screening

High-throughput identification of potent inhibitors. We optimize hit rates for standard binding pockets using advanced algorithms.

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Protein Drug Virtual Screening

Specialized screening for peptide therapeutics and biologics, accounting for flexibility and large surface interactions.

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Compound Library Design

Curate focused libraries tailored to your target. We filter for drug-likeness and diversity to maximize efficiency.

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Multiple-target Virtual Screening

Address polypharmacology and repurposing by screening compounds against multiple targets simultaneously.

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Ready to screen?

Discover the perfect library for your target. Our catalog covers comprehensive specifications for Bioactive, Natural Product, and Fragment libraries tailored for drug discovery.

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Our Virtual Screening Service Capabilities

We employ advanced algorithms and high-performance computing to offer comprehensive computational screening services. Select a service below to learn more.

Inverse Virtual Screening Service

Target Identification & Drug Repositioning
Identify potential protein targets for a given small molecule with our advanced "Target Fishing" approach. Our inverse screening (Reverse Docking) platform screens your compound against a vast database of the druggable proteome.

This service is critical for drug repositioning, elucidating the mechanism of action for phenotypic hits, and predicting potential toxicity by identifying off-target interactions early in the discovery process.

Ligand-based Virtual Screening (LBVS)

Screening Without Structure
Ideally suited for targets where the crystal structure is unavailable or highly flexible. We leverage the chemical features of known active ligands to identify novel hits.

By utilizing shape similarity search, molecular fingerprinting, and advanced QSAR modeling, we can efficiently enrich compound libraries with scaffolds that possess high structural or electrostatic similarity to your reference compounds.

Structure-based Virtual Screening (SBVS)

High-Precision Molecular Docking
When the 3D structure of the target is available, our SBVS service provides the most direct method for hit identification. We utilize high-performance docking algorithms to predict the preferred binding orientation and affinity of millions of small molecules.

Our workflow includes ensemble docking to account for protein flexibility and consensus scoring to minimize false positives, delivering a high-quality list of candidates for experimental testing.

Fragment-based Virtual Screening

Exploring Chemical Space Efficiently
Screening low molecular weight compounds (fragments) allows for a more efficient exploration of chemical space compared to HTS. This method is particularly effective for "undruggable" or challenging targets.

We identify weak but specific binders with high ligand efficiency, which can then be grown or linked into potent lead compounds using structural guidance, offering a robust starting point for lead generation.

Pharmacophore-based Virtual Screening

Scaffold Hopping & abstract Design
We construct precise 3D pharmacophore models defined by the spatial arrangement of essential features (hydrogen bond donors/acceptors, hydrophobic regions) required for binding.

This abstract method is powerful for "scaffold hopping," allowing us to identify structurally diverse chemotypes that share the same biological activity profile but possess improved physicochemical properties or novel intellectual property positions.

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Compound Databases Available for Screening

Access our diverse and high-quality compound libraries, ranging from bioactive molecules to fragment-based collections.

Library Category	Available Collections & Specifications
Bioactive Compound Libraries	Bioactive Compound Library Drug Repurposing Compound Library Featured Novel Bioactive Compound Library Disease-Specific Collections Target-Focused Libraries (GPCR, Kinase, etc.) Approved Drug Library
Natural Product Libraries	Disease-Functional Natural Products Activity-classified Natural Product Library Structure-classified Natural Product Library Natural Product Derivatives Libraries High-Throughput Screening (HTS) Natural Products
Drug-Like Compound Libraries	High-Diversity Drug-Like Library CNS-Penetrant Library Macrocyclic Compounds Potential Disease Targets Pathway-Focused Screening Sets
Fragment Libraries	General Fragment Library (Ro3 Compliant) Drug-Fragment Library High Solubility 3D Diversity Fragment Library Featured Fragments High Solubility Micro Fragment Library Carboxylic Acid Fragment Library Mini Electrophilic Heterocyclic Fragment Library

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Virtual Screening Workflow and Methodology

A systematic in silico screening workflow ensures the efficient identification of high-quality hits from compound libraries.

1. Library Preparation

Curation of small molecule libraries (e.g., ZINC, ChEMBL, or custom libraries). Filtering for drug-like properties (Lipinski's Rule of 5) and ADMET criteria.

2. Target Analysis

Binding pocket identification and preparation. We analyze the receptor for druggability and flexibility to ensure accurate docking.

3. Docking & Scoring

High-throughput docking of millions of compounds. We use advanced scoring functions to rank compounds based on predicted binding affinity.

4. Hit Selection

Post-screening analysis including visual inspection of binding modes and hit prioritization for experimental validation.

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From In Silico Hits to Wet-Lab Evidence

Experimental Validation Support After Virtual Screening

After virtual screening, many clients need to know whether the predicted hits are testable, purchasable, biologically active, and suitable for downstream optimization. To make screening results more actionable, we can support follow-up validation through assay design guidance, compound selection, biochemical testing coordination, cell-based evaluation, and integrated data interpretation.

Why validation matters

Make virtual screening results experimentally actionable

Docking scores and computational rankings are useful for prioritization, but they do not replace biological testing. A stronger discovery workflow should connect predicted binding with measurable activity, selectivity, and developability.

Confirm whether top-ranked hits show real target activity
Reduce false positives from docking or scoring bias
Prioritize compounds for purchase, synthesis, or analog expansion
Generate data for hit-to-lead optimization decisions

Biochemical Activity Assays

Support includes: enzyme inhibition, receptor binding, protein-ligand interaction, kinase activity, protease activity, or target-specific biochemical assay planning for prioritized compounds.

Cell-Based Functional Validation

Support includes: cell viability, pathway activity, reporter assays, antiviral activity, phenotypic readouts, target engagement, and preliminary dose-response evaluation.

Hit Confirmation and Dose-Response Testing

Support includes: confirmation testing for selected hits, IC₅₀/EC₅₀ estimation, replicate testing, positive/negative control selection, and preliminary SAR interpretation.

Selectivity and Counter-Screening

Support includes: related-target comparison, off-target risk evaluation, orthogonal assay planning, cytotoxicity counterscreens, and prioritization of compounds with cleaner activity profiles.

Integrated computational and experimental decision support: top virtual screening hits can be further evaluated through molecular docking, molecular dynamics simulation, in silico ADMET prediction, and wet-lab validation planning. This helps clients move from a computational hit list to a more reliable experimental shortlist.

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Deliverables from Virtual Screening Projects

We provide comprehensive data and reports to facilitate your downstream experimental assays.

Ranked Compound List: A prioritized list of hits with docking scores and calculated binding energies.
Docking Poses: 3D coordinates of the predicted binding modes for the top hits (PDB/SDF format).
Screening Report: A detailed report describing the methodology, target preparation, library details, and analysis of top interactions.
Interaction Analysis: 2D and 3D visualization of key protein-ligand interactions.

Virtual Screening Service FAQs

Do you offer follow-up optimization services?

What Are Major Design Considerations for Virtual Screening?

Successful virtual screening is a balance of multiple technical factors:

Target Selection: Using high-resolution structures or high-confidence AlphaFold2/homology models.
Pharmacophore Constraints: Incorporating known key interactions (e.g., H-bonds with catalytic residues) to prioritize relevant binding modes.
Chemical Space: Balancing library diversity with targeted sets (e.g., covalent warhead libraries or CNS-focused sets).
Property Filtering: Early removal of REOS, PAINS, and non-drug-like molecules to ensure the developability of identified hits.

How do you handle target flexibility in virtual screening?

Target flexibility is a major challenge in drug discovery. We address this using several advanced computational strategies:

Ensemble Docking: Screening against multiple protein conformations derived from different crystal structures or MD simulation snapshots.
Induced Fit Docking (IFD): Allowing active site side-chains to rearrange and optimize their positions upon ligand binding.
Covalent Docking: Specialized algorithms for targets where the ligand forms a chemical bond with a flexible residue (e.g., Cysteine).

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