CADD Consulting provides boutique computational services around scientific core competencies:
- Structure Analysis
- Computer-Aided Drug Design
- AI-Based Structure Prediction
- MD & Protein Design
- Rapid Custom Tooling
- Cheminformatics Services
- Large-Scale Docking
- Compute Infrastructure
Computer-aided drug design is hard to do well — the methods are intricate, the software takes years to master, and experienced specialists are scarce. CADD Consulting brings that expertise to your project directly: deep domain knowledge in chemistry, structural and computational biology, and modern AI, paired with fast, confidential turnaround on dedicated in-house infrastructure. We work as an embedded extension of your team, from one-off structural questions to sustained discovery support.
Structure Analysis
Good molecule design starts with understanding the target in detail. CADD Consulting analyzes and predicts protein and protein–ligand structures — and turns them into clear, shareable 3D visualizations that get your whole team working from the same picture. Seeing exactly where and how a ligand binds surfaces design ideas that a table of numbers keeps hidden.
Computer-Aided Drug Design
Computer-aided drug design turns structural and chemical insight into concrete decisions: which analog to make next, which series to pursue, which modification will improve potency or selectivity. CADD Consulting pairs state-of-the-art modeling software with deep medicinal-chemistry and structural-biology expertise to guide those calls — from hit identification through lead optimization. The result is fewer wasted synthesis cycles and faster progress toward a candidate.
AI-Based Structure Prediction
Deep learning methods such as AlphaFold3 and its open-source alternatives have transformed how we predict protein structures and protein-ligand interactions. CADD Consulting leverages these AI-based cofolding and structure prediction tools — alongside protein language models for antibody design — to complement classical modeling approaches. We run these models on dedicated in-house GPU infrastructure, enabling fast iteration and full data confidentiality. We help you assess when AI predictions are reliable, where they fall short, and how to integrate them into your drug design workflow.
Molecular Dynamics & Protein Design
Understanding a protein’s static structure is only half the story. CADD Consulting runs GPU-accelerated molecular dynamics simulations to reveal how proteins move and adapt — characterizing binding site flexibility, conformational ensembles, and the stability of protein–ligand and antibody–antigen complexes.
We also combine physics-based methods with AI-driven generative approaches to engineer proteins, peptides, and antibodies with improved properties — and validate the results computationally before you commit to the bench.
Rapid Custom Tooling
Off-the-shelf software rarely fits a discovery project exactly. CADD Consulting builds custom cheminformatics and modeling workflows around your data — and deploys and operationalizes tools like OpenFE and Boltz directly in your environment, training your team to run them independently. Deep domain knowledge plus AI-accelerated engineering means validated tooling in days, not months — and when data must stay in-house, we run fully on local infrastructure.
Cheminformatics
Most teams already have far more compound data than they can keep in check — an HTS collection in the tens or hundreds of thousands — yet still prioritize by eye, a handful at a time. CADD Consulting brings order to it: calculating properties, filtering, clustering, and enumerating analogs to tag your whole collection and surface the best few hundred worth pursuing — on solid criteria instead of gut feel. Everything is scripted and reproducible (RDKit, Python) — easy to trace, tune, and rerun as your data grows.
Large-Scale Docking
Large-Scale Docking screens between one million to multiple billion molecules in silico. Ingredients for a successful screen:
- Good protein structure
- Positive controls: ideally X-ray
- Library of synthesizable molecules
- Experience in docking analysis
- Hardware and software
- Assays to test binding or inhibition
We are experts and excited to run large-scale docking screens on your target.
Compute Infrastructure
Most of our work runs on dedicated high-performance hardware: a 64 core Threadripper PRO workstation with two NVIDIA RTX 3090 GPUs (24 GB VRAM each), 256 GB RAM, and fast SSD storage, managed through Proxmox with GPU-passthrough VMs. This setup powers our AI-based structure prediction (AlphaFold3, Boltz-2), molecular dynamics simulations, and large-scale docking — with fast turnaround and full data confidentiality. For projects that exceed local capacity, we scale professionally to the cloud.