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TIM-barrel

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laplacian (3)
adjacency-matrix (2)
CW-complex (2)
self-attention (2)
kolmogorov-complexity (1)
asymptotic-equipartition-property (1)
mutual-information (1)
entropy (1)
simplicial-complex (1)
simplicial-surface (1)
manifold-complex (1)
combinatorial-surface (1)
csaszar-polyhedron (1)
Math (1)
PGMs (1)
Sampling (1)
Algebraic-topology (1)
homeomorphism (1)
deformation-retraction (1)
mapping-cylinder (1)
quotient-space (1)
homotopy (1)
homotopic-maps (1)
retraction (1)
idempotent (1)
homotopy-rel-A (1)
inclusion (1)
homotopy-equivalence (1)
homotopy-equivalent (1)
homotopy-type (1)
contractible (1)
nullhomotopic (1)
genus (1)
dimension (1)
topological-graph (1)
euler-characteristic (1)
real-projective-space (1)
complex-projective-space (1)
characteristic-map (1)
subcomplex (1)
CW-pair (1)
product-space (1)
suspension (1)
join (1)
simplex (1)
radial-projection (1)
wedge-sum (1)
smash-product (1)
isomorphic (1)
fundamental-group (1)
reduced-suspension (1)
attach (1)
mapping-cone (1)
graph (1)
scopolamine (1)
benztropine (1)
FSCV (1)
methylphenidate (1)
IC50 (1)
IDS (1)
EDS (1)
t-test (1)
ANOVA (1)
tukeys-post-hoc (1)
fishers-LSD (1)
sidaks-correction (1)
two-way-ANOVA (1)
kolmogorov-smirnov-test (1)
ibogaine (1)
intra-peritoneal (1)
ASST (1)
GBR12909 (1)
rimcazole (1)
JHW007 (1)
pyrovalerone (1)
5HT2a (1)
5HT2b (1)
GPCR (1)
kinase (1)
GNA (1)
PNA (1)
TNA (1)
codon (1)
value (1)
key (1)
query (1)
attention-weights (1)
dot-prod-sa (1)
scaled-dot-prod-sa (1)
multi-head-sa (1)
transformer-layer (1)
operon (1)
sgRNA (1)
SpCas9 (1)
linear-transformer (1)
FWP (1)
update-rule (1)
delta-rule (1)
fast-weights (1)
slow-weights (1)
outer-product (1)
tensor-product-representation (1)
softmax-kernal (1)
symbolic-structure (1)
role (1)
filler (1)
attention-normalisation (1)
katharopoulos-linear-attention (1)
FAVOR (1)
DPFP (1)
capacity-control (1)
BLEU (1)
perplexity (1)
delta-network (1)
ablation-study (1)
tied-proteinMPNN (1)
Win1 (1)
4Mu-Ac (1)
Janus1 (1)
Janus2 (1)
michaelis-menton (1)
4Mu-PhAc (1)
Janus3 (1)
Mu-N-Ac (1)
SEC (1)
monodisperse (1)
SPR (1)
streptavidin-biotin (1)
Ras-GTP (1)
MoE (1)
KDA (1)
MLA (1)
AttnRes (1)
LatentMoE (1)
MoonViT-V2 (1)
Muon (1)
Design (1)
Ownership (1)
VLA-model (1)
world-model (1)
world-action-model (1)
bit-equivalent (1)
probability-space (1)
bandit-environment (1)
nat (1)
data-processing-inequality (1)
kernelized-bandit-optimization (1)
gaussian-process (1)
mercer-decomposition (1)
spectral-tail (1)
matern-kernel (1)
squared-exponential-kernel (1)
thompson-sampling (1)
fixed-truncation (1)
GP-UCB (1)
RFdiffusion (1)
anfinsens-hypothesis (1)
PDB (1)
activation-maximization (1)
Chroma (1)
escherichia-coli (1)
masked-language-models (1)
3D-crystal (1)
1D-fibre (1)
2D-lattice (1)
9OP9 (1)
NCAA (1)
beta-barrel (1)
Top7 (1)
TIM-barrel (1)
protein-language-models (1)
rosetta (1)
nanopore (1)
macrocycle (1)
oligoamide (1)
BindCraft (1)
ProGen (1)
PXDesign (1)
affinity (1)
TNF (1)
scFv (1)
VHH (1)
CDR (1)
HELM-GPT (1)
RFpeptides (1)
IDR (1)
PepPrCLIP (1)
affinity-handle (1)
beta-catenin (1)
SS18-SSX1 (1)
beta-amyloid (1)
tau-protein (1)
glycoproteins (1)
oligomerization (1)
FGF (1)
endocytosis (1)
transcytosis (1)
EndoTags (1)
digoxigenin (1)
methotrexate (1)
CID (1)
kemp-elimination (1)
retro-aldol (1)
luciferase (1)
PLACER (1)
serine (1)
CRISPR-Cas (1)
zinc-fingers (1)
Product (1)
System-Design (1)

Published on
September 17, 2026
The past, present and future of de novo protein design
RFdiffusion anfinsens-hypothesis PDB activation-maximization Chroma escherichia-coli masked-language-models 3D-crystal 1D-fibre 2D-lattice 9OP9 NCAA beta-barrel Top7 TIM-barrel protein-language-models rosetta nanopore macrocycle oligoamide BindCraft ProGen PXDesign affinity TNF scFv VHH CDR HELM-GPT RFpeptides IDR PepPrCLIP affinity-handle beta-catenin SS18-SSX1 beta-amyloid tau-protein glycoproteins oligomerization FGF endocytosis transcytosis EndoTags digoxigenin methotrexate CID kemp-elimination retro-aldol luciferase PLACER serine CRISPR-Cas zinc-fingers
Research notes on The past, present and future of de novo protein design.
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TIM-barrel

TIM-barrel (1)

The past, present and future of de novo protein design