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Solo Journal Club
Working through 32 papers in the protein ML space — from coevolutionary models to diffusion-based design. Sorted from foundational to frontier. Each paper gets a full discussion page with historical context, key takeaways, and honest caveats.
Discussed
#1
Potts Hamiltonian Models of Protein Co-variation, Free Energy Landscapes, and Evolutionary Fitness
Levy, Haldane, Flynn ·
Curr Opin Struct Biol
2017 · Review
Discussed
#2
Reverse Distillation: Consistently Scaling Protein Language Model Representations
Catrina, Bepler, Sledzieski, Singh ·
ICLR
2026
Discussed
#3
Assessing the Utility of Coevolution-based Residue-Residue Contact Predictions (GREMLIN)
Kamisetty, Ovchinnikov, Baker ·
PNAS
2013
Discussed
Upcoming
#4
DeepLIFT: Learning Important Features Through Propagating Activation Differences
Shrikumar et al. · 2017
Upcoming
#5
SurfProp: Surface-based Property Prediction for Antibody Developability
Rao et al. · 2023
Upcoming
#6
State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold
Roney et al. ·
Phys Rev Lett
2022
Upcoming
#7
EigenFold: Generative Protein Structure Prediction with Diffusion Models
Jing et al. · 2023
Upcoming
#8
AlphaFold2 Has More to Learn About Protein Energy Landscapes
Chakravarty et al. · 2023
Upcoming
#9
Assessment of AlphaFold Protein Models for Small-Molecule Ligand Docking
Maidanik et al. · 2026
Upcoming
#10
Enhanced Diffusion Sampling: Efficient Rare Event Sampling with Diffusion Models
Xie et al. · 2026
Upcoming
#11
Ibex: Pan-immunoglobulin Structure Prediction
Dreyer et al. · 2025
Upcoming
#12
Predicting Specificity of TCR-pMHC Interactions
Culka et al. · 2025
Upcoming
#13
Millisecond Prediction of Protein Contact Maps from Amino Acid Sequences
Lin et al. · 2026
Upcoming
#14
Test-Time Training Done Right
Zhang et al. · 2025
Upcoming
#15
Detection of Protein Symmetry and Structural Rearrangements via SSE
Lin et al. · 2025
Upcoming
#16
mBER: Controllable de novo Antibody Design with Million-Scale Screening
Swanson et al. · 2025
Upcoming
#17
FAMPNN: Sidechain Conditioning for Full-Atom Protein Sequence Design
Shuai et al. · 2025
Upcoming
#18
Learning Hamiltonian Flow Maps for Large-Timestep Molecular Dynamics
Ripken et al. · 2026
Upcoming
#19
ConfDiff: Force-Guided SE(3) Diffusion for Protein Conformation Generation
Wang et al. · 2024
Upcoming
#20
FrameDiff: SE(3) Diffusion Model for Protein Backbone Generation
Yim et al. · 2023
Upcoming
#21
AF2BIND: Predicting Small-Molecule Binding Sites Using AlphaFold2
Gazizov et al. ·
Nat Methods
2026
Upcoming
#22
VoxMol: 3D Molecule Generation by Denoising Voxel Grids
Pinheiro et al. · 2023
Upcoming
#23
Compressing the Collective Knowledge of ESM into a Single Protein Language Model
Dinh et al. ·
Nat Methods
2026
Upcoming
#24
ProteinMPNN: Robust Deep Learning Based Protein Sequence Design
Dauparas et al. · 2022
Upcoming
#25
Scaling Atomistic Protein Binder Design with Generative Pretraining
Didi et al. (Proteina-Complexa) · 2026
Upcoming
#26
ProteinEBM: Protein Diffusion Models as Statistical Potentials
Roney, Ou, Ovchinnikov · 2025
Upcoming
#27
Toward Machine-Guided Design of Proteins
Biswas et al. · 2018
Upcoming
#28
BioEmu: Scalable Emulation of Protein Equilibrium Ensembles
Lewis et al. · 2024
Upcoming
#29
Synonymous Mutations in Representative Yeast Genes Are Mostly Strongly Non-Neutral
Shen et al. ·
Nature
2022
Upcoming
#30
ProteinTTT: One Protein Is All You Need
Bushuiev et al. · 2026
Upcoming
#31
Protein Hunter: Exploiting Structure Hallucination for Protein Design
Cho et al. · 2025
Upcoming
#32
Latent Generative Search for de novo Biomolecular Interactions at Scale
Didi et al. (Proteina-Complexa validation) · 2026
Upcoming