marc@mdeller:~$ whoami
Marc C. Deller, D.Phil.
— Structural biologist working in drug discovery. This is where the tools I build end up: small web apps for people who work with protein structures. Free, no sign-up, nothing to install.main site → marcdeller.com "Hidden Architecture: Mapping Biology’s Structure"
marc@mdeller:~$
ls -la apps/
# 19 live, 0 building- ●DEBRIS # every DOI-verified paper that puts a micro or nanoplastic particle inside a human disease, read by one fine-tuned 3B model and mapped four ways: a polymer Venn over an evidence ladder, a clickable body map, a pathway hub and a live feed of the papers. 9,323 papers verified against Crossref, with the tagger recording polymer, organ system, mechanism, study design and how far each claim sits from an effect in a living person github.com/bellcheddar/DEBRIS
- ●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 annotation. 285,996 bridges, 15,804 of them in none of the three curated glue databases, resolving into 82 protein pairs that each carry a medicinal chemistry series nobody has written up github.com/bellcheddar/BINMAN
- ●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 on the backbone github.com/bellcheddar/PODIUM
- ●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 its closest relatives actually tried and how far each got github.com/bellcheddar/FAFFAbout
- ●GATECRASHER # four published drug discovery campaigns in one shell: the pocket, the SAR, every designed edit, and the structural basis of selectivity github.com/bellcheddar/GATECRASHER
- ●PUNT # A fantasy football companion for a ten-team bar league: live spoken commentary, win probability, playoff odds and a Monday card pack github.com/bellcheddar/PUNT
- ●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-shaped units, a base model with no fine-tuning, and a decline when the corpus genuinely does not know github.com/bellcheddar/chatMCD
- ●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 github.com/bellcheddar/GOBSMACKED
- ●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 them, with no multiple sequence alignment anywhere github.com/bellcheddar/ALPHABETTI
- ●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 web version of PhoneFold github.com/bellcheddar/ButtFold
- ●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 github.com/bellcheddar/CODSWALLOP
- ●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 github.com/bellcheddar/TopPDBLX
- ●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 trajectory analysis github.com/bellcheddar/FlexAppeal
- ●AlphaFraud # Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures github.com/bellcheddar/AlphaFraud
- ●BoltzMaker # Build and analyze Boltz-2 protein structure prediction campaigns: a guided input wizard, YAML generation, and full result analysis with confidence/affinity dashboards -- no GPU required github.com/bellcheddar/BoltzMaker
- ●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 calls for structural truth. github.com/bellcheddar/chatPDB
- ●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 github.com/bellcheddar/ChemSage
- ●MicroPlastics Blaster # A browser-based arcade game by Elora Therapeutics — the biotech developing first-in-class enzyme therapy to remove microplastics from the human body. Fire enzymatic blasts at incoming polymer particles, protect the cell, and climb the global leaderboard github.com/bellcheddar/microplastic-blaster
- ●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 industrial reactor, with predicted structures superposed on IsPETase and the catalytic triad highlighted github.com/bellcheddar/PANTS
marc@mdeller:~$ top -bn1 | head
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marc@mdeller:~$ cat links.txt
blog structural-biology publications structures projects patents vibe-coding about-me