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Platform Playbook

Build it yourself.

The practical route: build the lab, pick the CRO, run the pipeline, then use the tools behind it. Ends with a way to work with Marc.

In reading order

Build it yourself 9 Tools and pipelines 20

Try it

mdeller.com chatMCD ↗ Ask about Marc C. Deller and get an answer in the third person, drawn from his own papers, patents, thesis and notes: hybrid retrieval over … mdeller.com GOBSMACKED ↗ fold, dock, relax and annotate a protein-ligand complex on your own GPU, then find the crystal structure and get graded on how close you got… mdeller.com FlexAppeal ↗ Set up protein molecular dynamics without writing the script: every OpenMM option explained, a self-contained bundle to run on your own mach… mdeller.com BoltzMaker ↗ Build and analyze Boltz-2 protein structure prediction campaigns: a guided input wizard, YAML generation, and full result analysis with conf… mdeller.com ChemSage ↗ A hybrid, chemically aware LLM for drug discovery: RAG for facts, a QLoRA-tuned model for behavior, and live RDKit/PyMOL tool calls for chem…

Build it yourself

9 articles
9 Sep 2025 · 2 min read Building a Comprehensive Protein Production, X-ray Crystallography, and Cryo-EM Laboratory from Scratch Building a Comprehensive Protein Production, X-ray Crystallography, and Cryo-EM Laboratory from Scratch https://marcdeller.com/wp-content/uploads/2025/09/glacios_540p.mp4… 20 Aug 2025 · 4 min read Unlocking Protein Structure Insights without a Lab: Harnessing CRO Services for Structural Biology Research Unlocking Protein Structure Insights without a Lab: Harnessing CRO Services for Structural Biology Research CRO partnerships: eliminate the need for costly internal lab i… 13 Aug 2025 · 3 min read The Self-Driving Lab: How Automation and AI Are Redefining the Pace of Discovery The Self-Driving Lab: How Closed-Loop AI and Robotics Are Reshaping Drug Discovery The Big Benefits of Going Small: Novartis Mic-Drop and MicroCycle Closed-loop autonomy:… 22 Aug 2025 · 2 min read Unveiling FragLites: Pioneering Precision in Drug Discovery Unveiling FragLites: Pioneering Precision in Drug Discovery FragLites are a focused library of 31 halogenated fragments used to map protein binding sites with high sensit… 7 Dec 2025 · 3 min read Self-Encoded Libraries: A New Era in Drug Discovery Screening Self-Encoded Libraries: A New Era in Drug Discovery Screening Barcode-free hit discovery from massive libraries enabled by automated small molecule structure annotation S… 27 Aug 2025 · 2 min read Empowering QSAR Modeling: Optimal Data Practices and Cutting-Edge Tools Empowering QSAR Modeling: Optimal Data Practices and Cutting-Edge Tools Dataset Curation: Assemble diverse, high-quality chemical–activity pairs from public databases, ap… 22 Aug 2025 · 2 min read MARCUS: Revolutionizing Chemical Literature Curation with AI-Driven Annotation and Recognition MARCUS: Revolutionizing Chemical Literature Curation with AI-Driven Annotation and Recognition MARCUS seamlessly integrates text annotation with multi-engine optical chem… 8 Jul 2026 · 20 min read BoltzMaker: Vibe-Coding a Campaign-Scale Boltz-2 Pipeline BoltzMaker: Vibe-Coding a Campaign-Scale Boltz Pipeline BoltzMaker: Boltz2 campaign-scale structure and affinity prediction, binding analysis, and run control, orchestrat… 30 Jun 2026 · 12 min read ChemSage: Vibe-Coding a Chemically Aware Drug-Discovery LLM on Local Hardware ChemSage: Vibe-Coding a Chemically Aware Drug-Discovery LLM on Local Hardware ChemSage: a retrieval layer feeds corpus context to a QLoRA-tuned model whose tool calls are…

Tools and pipelines

20 articles
21 Jul 2026 · 27 min read AlphaFraud: Weekly watcher: newly deposited human PDB structures vs their blind AlphaFold predictions — a running test of whether protein folding is solved AlphaFraud Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures. 🌐 App alphafraud.mdeller.com ✉️ Contact marc@marcdeller.… 25 Jul 2026 · 6 min read ChatPDB: A protein-structure-literate AI assistant for the Protein Data Bank: RAG for facts, a QLoRA-tuned model for behaviour chatPDB A protein-structure-literate AI assistant for the Protein Data Bank: RAG for facts, a QLoRA-tuned model for behaviour, and live Biopython/gemmi/DSSP/PyMOL tool ca… 15 Sep 2026 · 47 min read TopPDBLX: Every PDB crystallisation condition, parsed and indexed against his own JCSG Top96 taxonomy TopPDBLX Every crystallisation condition in the Protein Data Bank, parsed, normalised and linked to the sequence that produced it. 🌐 App toppdblx.mdeller.com ✉️ Contact m… 15 Sep 2026 · 45 min read CODSWALLOP: Every PDB entry for a protein family: what was made, what it bound, what crystallised CODSWALLOP The PDB, summarised: every entry for a protein family, cross-referenced in ninety seconds. 🌐 App codswallop.mdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub… 15 Sep 2026 · 18 min read FAFFAbout: A small LLM trained on the PSI TargetTrack archive, forecasting which targets crystallise and which fail FAFFAbout Fine-tuned Attrition Forecasting From Archives: know where your protein is likely to die before you order the gene. 🌐 Website marcdeller.com ✉️ Contact marc@mar… 15 Sep 2026 · 35 min read GOBSMACKED: fold, dock, relax and annotate a protein-ligand complex, then grade it against the real crystal structure GOBSMACKED Fold, dock, relax and annotate a protein-ligand complex, then check it against the experimental structure. 🌐 App gobsmacked.mdeller.com ✉️ Contact marc@marcdel… 15 Sep 2026 · 12 min read FlexAppeal: An OpenMM-powered molecular dynamics pipeline: submit a protein, run it, watch its flexibility unfold FlexAppeal Turn the whole OpenMM option surface into a form, run the simulation on your own machine, and explore what comes back. 🌐 App flexappeal.mdeller.com ✉️ Contact … 15 Sep 2026 · 10 min read ALPHABETTI: A protein sequence logo in 3D, wrapped around its own ESMFold-predicted structure ALPHABETTI A protein sequence logo, in three dimensions, wrapped around its own predicted structure. 🌐 App alphabetti.mdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub … 15 Sep 2026 · 9 min read ButtFold: A protein folds in your browser and the trajectory becomes music: PhoneFold’s web sibling ButtFold A protein folds in your browser and the trajectory becomes music. 🌐 App buttfold.mdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/ButtFold ButtFol… 15 Sep 2026 · 54 min read PANTS: Mines metagenomes for uncharacterised PETase and MHETase candidates, ranked by catalytic triad and oxyanion hole PANTS Find PET-degrading enzymes that work at 37 °C in serum, not at 70 °C in a reactor. 🌐 App pants.mdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/PANTS… 10 Jul 2026 · 37 min read BoltzMaker: Boltz2 campaign-scale structure and affinity prediction, and binding analysis BoltzMaker BoltzMaker: Boltz2 campaign-scale structure and affinity prediction, binding analysis, and run control, orchestrated end to end from a single spec file. Read t… 1 Jul 2026 · 28 min read ChemSage: A hybrid, chemically aware LLM for drug discovery: RAG for facts, a QLoRA-tuned model for behavior ChemSage A hybrid, chemically aware LLM for drug discovery: RAG for facts, a QLoRA-tuned model for behaviour, and live RDKit/PyMOL tool calls for chemical truth. Fine-tun… 14 Jun 2026 · 3 min read FoldForge: Browser GUI for the whole Boltz-2 workflow ForgeFold A single-file browser GUI for the whole Boltz-2 workflow: build, run, review. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/FoldF… 14 Jun 2026 · 3 min read Boltz2Run: Every run logged, timed, and reproducible run_boltz.zsh A minimal, auditable wrapper for Boltz-1/2. Every run logged, timed, and reproducible. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bell… 14 Jun 2026 · 2 min read Smiles2YAML: From a JSON of candidate SMILES to a folder of Boltz-2 input YAML generate_yaml.py From a JSON of candidate SMILES to a folder of Boltz-2 input YAMLs, in one prompt. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellc… 14 Jun 2026 · 3 min read AnalyzeBoltz: Harvest the sprawling Boltz2 output tree, tidy summary, CSV, and CIF output folder analyze_boltz.py Harvest a sprawling Boltz-2 output tree into one tidy summary, CSV, and CIF folder. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bell… 14 Jun 2026 · 4 min read cif2plip: Protein-ligand interaction profiling using PLIP for co-folding outputs which produce CIF files cif2plip CIF to strict PDB to PLIP. Trustworthy interaction profiling for co-folding outputs. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar… 14 Jun 2026 · 9 min read ChatMol: Natural-language control of PyMOL, describe the scene, get the picture ChatMol Natural-language control of PyMOL. Describe the scene, get the structure. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/chatmol A n… 14 Jun 2026 · 2 min read PocketTide: An interactive dashboard for GLP-1R structures PocketTide An interactive dashboard for GLP-1R structures. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/PocketTide PocketTide is a browser… 14 Jun 2026 · 1 min read GPCR Binning: Structural binning and organisation utilities for GPCR datasets GPCR Binning Structural binning and organisation utilities for GPCR datasets. 🌐 Website marcdeller.com ✉️ Contact marc@marcdeller.com 🐙 GitHub bellcheddar/gpcr-binning GP…

Every tool on mdeller.com

18 live web apps
mdeller.com ALPHABETTI ↗ a protein sequence logo in 3D, wrapped around its own predicted structure. The amino acid letters themselves, stacked by how strongly a language model expects t… Read the write-up →
mdeller.com AlphaFraud ↗ Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures Read the write-up →
mdeller.com BINMAN ↗ an atlas of the molecular glues already sitting in the PDB: every ligand that buries surface against two protein chains at once, found by geometry rather than a…
mdeller.com BoltzMaker ↗ Build and analyze Boltz-2 protein structure prediction campaigns: a guided input wizard, YAML generation, and full result analysis with confidence/affinity dash… Read the write-up →
mdeller.com ButtFold ↗ a protein folds in your browser and the trajectory becomes music: contacts forming are note onsets, hydropathy sets pitch, secondary structure sets texture. The… Read the write-up →
mdeller.com CODSWALLOP ↗ every PDB entry for a protein family in one place: what was actually made, what it bound, what crystallised, and which residues nobody has ever seen Read the write-up →
mdeller.com ChatPDB ↗ A protein-structure-literate AI assistant for analyzing proteins: RAG for facts, a QLoRA-tuned model for behaviour, and live Biopython/gemmi/DSSP/PyMOL tool cal… Read the write-up →
mdeller.com ChemSage ↗ A hybrid, chemically aware LLM for drug discovery: RAG for facts, a QLoRA-tuned model for behavior, and live RDKit/PyMOL tool calls for chemical truth Read the write-up →
mdeller.com DEBRIS ↗ every DOI-verified paper on micro and nanoplastics in human disease, read by a fine-tuned 3B model and mapped by polymer, tissue, mechanism and strength of evid…
mdeller.com FAFFAbout ↗ forecasts where a protein is likely to stall on the road to a structure, from 335,771 real attempts in the Protein Structure Initiative archive, and shows what … Read the write-up →
mdeller.com FlexAppeal ↗ Set up protein molecular dynamics without writing the script: every OpenMM option explained, a self-contained bundle to run on your own machine, and interactive… Read the write-up →
mdeller.com GATECRASHER ↗ four published drug discovery campaigns in one shell: the pocket, the SAR, every designed edit, and the structural basis of selectivity
mdeller.com GOBSMACKED ↗ fold, dock, relax and annotate a protein-ligand complex on your own GPU, then find the crystal structure and get graded on how close you got, and why Read the write-up →
mdeller.com NOBBLE ↗ whether a molecular glue actually creates the interface it is credited with: every predicted ternary complex scored against 285,996 experimentally observed brid…
mdeller.com PANTS ↗ PETase ANnotation and Triage System: mines metagenomic sequence space for PET-degrading enzymes that work at 37 °C in serum rather than at 70 °C in an industria… Read the write-up →
mdeller.com PODIUM ↗ an interview deck in one live Mol* viewer: four selectivity campaigns, every contact measured by PLIP in the deposited structure, KLIFS and KRAS G-domain motifs…
mdeller.com TopPDBLX ↗ every crystallisation condition in the protein data bank, parsed and indexed: what worked, how often, and how little of it is specific to your protein Read the write-up →
mdeller.com chatMCD ↗ Ask about Marc C. Deller and get an answer in the third person, drawn from his own papers, patents, thesis and notes: hybrid retrieval over 3,643 question-shape…

Work with Marc

Marc C. Deller builds structural biology and protein science capability: labs, pipelines, CRO networks and the structure-based decisions that come out of them.

About Marc marcdeller.com Publications