Conducting Multiomics Analysis on Revilico OS
I want to conduct multiomics analysis with the data I have available to get a better understanding of my desired indication before diving into computational chemistry workflows.
Target Identification
Scientists
scRNA Sequence Analysis • Alphafold • Openfold • Pocket Search
Understanding Disease Biology and Mechanisms on Revilico OS
I want to understand how my disease of interest works biologically (what pathways, mechanisms, and cellular programs are driving it) before committing to target selection or downstream drug discovery workflows.
Target Identification
Scientists
scRNA Sequence Analysis
Generate a 3D Structural Hypothesis for a Molecular Target
I have a molecular target (protein) without an experimentally resolved structure, and I want to obtain a 3D structural hypothesis suitable for analysis and structure based drug design and discovery.
Target Identification
Scientists
AlphaFold • OpenFold • Boltz Co-Folding
Identify Primary Molecular Target for Phenotypic Hit via Reverse Docking
I have a drug with demonstrated efficacy but unknown mechanism of action, and I want to identify its primary molecular target(s) to enable structure-based optimization and rational drug design.
Target Identification
Scientists
Virtual Screening • Pharmacophore Analysis • Protein-Ligand Molecular Dynamics • Absolute Binding Free Energy
Determining Optimal Therapeutic Strategy for Drugging a Molecular Target
I have identified a molecular target implicated in disease, and I want to determine the optimal therapeutic strategy/ mode of action (e.g., inhibition, activation, or allosteric modulation) to achieve the desired biological outcome.
Target Identification
Scientists
Alphafold • Openfold • Pocket Search • BoltzGen Co-Folding • scRNA Sequence Analysis • Protein in Water Molecular Dynamics • Virtual Screening • Pharmacophore Analysis
Identifying Druggable Binding Sites on Challenging “Undruggable” Targets
I have a molecular target without obvious or stable binding sites, and I want to identify druggable pockets suitable for structure based drug design.
Target Identification
Scientists
Pocket Search • Protein in Water Molecular Dynamics • Virtual Screening • Protein-Ligand Molecular Dynamics
Identifying the Best Therapeutic Cell Line for a Drug-Target Complex
I have a known drug (ligand) and a target (protein) complex with demonstrated efficacy, and I want to identify which cell line will show the best therapeutic response based on its molecular profile.
Target Identification
Scientists
scRNA Sequence Analysis
Compound-Protein Interaction Discovery at Scale
I want to run a multiplex screen to understand how large compound libraries interact with large protein libraries, but the full experimental matrix is too expensive and time-intensive.
Target Identification
Scientists
Virtual Screening • Boltz Co-Folding • Protein-Ligand Molecular Dynamics
ABFE//RBFE • Absolute Binding Free Energy • QSAR Modeling • Pharmacophore Analysis • Generative Chemistry • ADMET Predictions • Molecular Orbital Analysis
Protein Variant and Mutagenesis Validation at Scale
I want to run large-scale separation-of-function mutants on my target to validate ligand–protein interactions, but experimentally generating and testing all variants is too intensive.
Target Identification
Scientists
AlphaFold • OpenFold • Virtual Screening • Boltz Co-Folding • BoltzGen Co-Folding • Protein-Ligand Molecular Dynamics • Pharmacophore Analysis • Absolute Binding Free Energy • ABFE/RBFE
QSAR Modeling • scRNA Sequence Analysis • ADMET Predictions
Resolve Binding Mechanisms and Molecular Interactions from Experimental Activity Data
I have experimental binding or activity data, and I want to understand why these molecules behave the way they do: what interactions are driving binding, what mechanisms explain activity differences, and how this informs next design decisions.
Hit Discovery
Scientists
Virtual Screening • Pharmacophore Analysis • Protein–Ligand Molecular Dynamics • ABFE/RBFE
QSAR Modeling
Identify Hits That Match a Specific Binding Modality or Mechanism
I have a biological target, and I want to identify a set of hits that meet a specific mechanistic or chemical criterion, like specific modes of action: inhibition, activation, covalent binding, or other specialized mechanisms.
Hit Discovery
Scientists
Virtual Screening • Pharmacophore Analysis
Protein in Water Molecular Dynamics • Protein–Ligand Molecular Dynamics • Ligand–Membrane Molecular Dynamics • ABFE/RBFE
Prioritize a Compound Library Against a Target Using Virtual Screening
I have a biological target and a large compound library that would be expensive and time-consuming to screen experimentally. I want to computationally prioritize a smaller, higher-confidence subset of compounds before committing to HTS.
Hit Discovery
Scientists
Virtual Screening
Protein in Water Molecular Dynamics
Generate an Expanded Small-Molecule Library From Hit Compounds
I have an identified target and a set of initial hit compounds that bind well, and I want a new library for further testing with an expanded set of chemical hypotheses.
Hit to Lead
Scientists
Generative Chemistry
Optimize a Moderately Active Molecule for Potency, Selectivity, and Developability
I have a moderately active molecule, and I want to optimize it for higher potency, better selectivity, and improved developability.
Hit to Lead
Scientists
Pharmacophore Analysis • QSAR Modeling • Generative Chemistry • Virtual Screening
Protein–Ligand Molecular Dynamics • ABFE/RBFE
Refine an Initial Hit Set into a High-Confidence Subset
I have an initial set of hits from a virtual screen, but I want a refined set with fewer false positives and false negatives, validated by more robust, physics-based simulations.
Hit to Lead
Scientists
Virtual Screening • Protein-Ligand Molecular Dynamics • ABFE/RBFE
QSAR Modeling • Pharmacophore Analysis
Multi-Parameter Optimize a Moderately Active Molecule via Scaffold Decoration and Scaffold Hopping
I have a moderately active small molecule, and I want to improve it across multiple dimensions (potency, selectivity, developability, etc.) by exploring scaffold decoration and scaffold hopping, while preserving key motifs that drive favorable target interaction.
Hit to Lead
Scientists
Virtual Screening • Pharmacophore Analysis • Generative Chemistry
Protein-Ligand Molecular Dynamics • ABFE/RBFE
Metabolite-Inspired Drug Development & Allosteric Optimization
I have a binder to my protein, but I want to design synergistic or allosteric modulators to improve target engagement and reduce reliance on traditional, trial-and-error SAR campaigns.
Hit to Lead
Scientists
Virtual Screening • Protein-Ligand Molecular Dynamics • Protein in Water Molecular Dynamics • Generative Chemistry • Pharmacophore Analysis • Boltz Co-Folding • Absolute Binding Free Energy • ABFE/RBFE
QSAR Modeling • ADMET Predictions • Geometry Optimization • Molecular Orbital Analysis • scRNA Sequence Analysis
Deeply Characterize Lead Molecules Using Quantum Chemistry and Property Analysis
I have lead compounds, and I want a deeper understanding of their molecular properties, such as metabolic stability, conformational behavior, electronic structure, and physicochemical properties, to guide confident lead optimization decisions.
Lead Optimization
Scientists
Conformer Search • Geometry Optimization • Molecular Orbital Analysis • ADMET Predictions • Compound Solubility • Retrosynthesis
Understand On-Target and Off-Target Biological Pathway Engagement for Lead Compounds
I have a set of lead compounds, and I want to understand both their direct on-target effects and their indirect off-target effects, including how they engage broader biological pathways and cellular programs.
Lead Optimization
Scientists
Virtual Screening • scRNA Sequence Analysis
Boltz Co-Folding • BoltzGen Co-Folding
Assess Lead Toxicity Risk via Target-Based Computational Screening
I have a set of lead compounds, and I want to determine whether they are likely to be toxic by screening them against a panel of protein targets known to contribute to toxicity in my indication.
Lead Optimization
Scientists
Virtual Screening • Pharmacophore Analysis • ADMET Predictions
Protein in Water Molecular Dynamics • Protein-Ligand Molecular Dynamics
Multi-Parameter Optimization for Developability: Solubility, ADME, and Toxicity
I have a set of lead compounds, and I want to optimize them across multiple developability dimensions, like solubility, ADME, toxicity, and related properties, without losing on-target potency.
Lead Optimization
Scientists
ADMET Predictions • Compound Solubility • Generative Chemistry • Retrosynthesis
Conformer Search • Geometry Optimization • Molecular Orbital Analysis
Plan Synthetic Routes and Pathways for Lead Compounds
I have a set of lead compounds, and I want to plan practical synthetic routes and pathways so I can prioritize what to make next.
Lead Optimization
Scientists
Retrosynthesis
Geometry Optimization • Molecular Orbital Analysis • Conformer Search
Design Novel, Non-Infringing Chemical Matter with Comparable Performance
I have a set of lead compounds that infringe on existing patents. I need to design novel chemical matter that preserves favorable performance while avoiding infringement.
Lead Optimization
Scientists
Virtual Screening • Protein–Ligand Molecular Dynamics • Pharmacophore Analysis • ABFE/RBFE • ADMET Predictions • Compound Solubility • Conformer Search
Generative Chemistry • Retrosynthesis • Geometry Optimization • Molecular Orbital Analysis
Centralized Experimental and Computational Data Management
I want my data to live in one place where it is visible, usable, and computationally actionable.
Operations
Executives
Pipeline Transparency and Execution Oversight
I need to know what’s running, what failed, and what’s ready, without asking everyone.
Operations
Executives
Structured Knowledge Transfer
What happens if a key scientist leaves the project?
Operations
Executives
Reproducibility and Version Control
I need to reproduce last quarter’s results without guessing what settings were used.
Operations
Executives
Cross-Team Collaboration Without File Chaos
My chemists, computationalists, and biologists need to work together without breaking each other’s workflows.
Operations
Executives
