:: Library Catalog

Cover Image

Saved in:

Bibliographic Details
Main Authors:	Teufel, Felix, Kollasch, Aaron W., Huang, Yining, Winther, Ole, Yang, Kevin K., Notin, Pascal, Marks, Debora S.
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	https://arxiv.org/abs/2512.02315
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Multi-Scale Representation Learning for Protein Fitness Prediction
by: Zhang, Zuobai, et al.
Published: (2024)

Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction
by: Weitzman, Ruben, et al.
Published: (2025)

TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction
by: Cho, Seungik
Published: (2026)

Evolutionary Profiles for Protein Fitness Prediction
by: Fan, Jigang, et al.
Published: (2025)

Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
by: Yu, Ziyang, et al.
Published: (2024)

Mitigating Molecular Aggregation in Drug Discovery with Predictive Insights from Explainable AI
by: Sturm, Hunter, et al.
Published: (2023)

Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation
by: Kantroo, Pranav, et al.
Published: (2024)

Hermes: Large DEL Datasets Train Generalizable Protein-Ligand Binding Prediction Models
by: Kleinsasser, Maxwell, et al.
Published: (2026)

Protein FID: Improved Evaluation of Protein Structure Generative Models
by: Faltings, Felix, et al.
Published: (2025)

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
by: Wu, Lirong, et al.
Published: (2024)

Steering Generative Models with Experimental Data for Protein Fitness Optimization
by: Yang, Jason, et al.
Published: (2025)

Mechanisms of AI Protein Folding in ESMFold
by: Lu, Kevin, et al.
Published: (2026)

Improving Protein Optimization with Smoothed Fitness Landscapes
by: Kirjner, Andrew, et al.
Published: (2023)

DrugLLM: Open Large Language Model for Few-shot Molecule Generation
by: Liu, Xianggen, et al.
Published: (2024)

PLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction
by: Xu, Xingjian, et al.
Published: (2024)

Into the Unknown: From Structure to Disorder in Protein Function Prediction
by: Kolarić, Đesika, et al.
Published: (2025)

ProtScan: Modeling and Prediction of RNA-Protein Interactions
by: Corrado, Gianluca, et al.
Published: (2024)

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
by: Chen, Bo, et al.
Published: (2024)

PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL
by: Ford, Colby T., et al.
Published: (2025)

Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers
by: Wang, Yingheng, et al.
Published: (2024)

DeepFRI Demystified: Interpretability vs. Accuracy in AI Protein Function Prediction
by: Krishna, Ananya, et al.
Published: (2025)

SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
by: Ma, Runze, et al.
Published: (2024)

DeepRLI: A Multi-objective Framework for Universal Protein--Ligand Interaction Prediction
by: Lin, Haoyu, et al.
Published: (2024)

Atom-level Protein Representation Learning Improves Protein Structure Prediction
by: Kim, Taewon, et al.
Published: (2026)

Open-Source Protein Language Models for Function Prediction and Protein Design
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)

Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer
by: Huang, Tinglin, et al.
Published: (2024)

IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins (IDP) Using Large Language Models
by: Mollaei, Parisa, et al.
Published: (2024)

Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space
by: Lee, Minji, et al.
Published: (2024)

An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation
by: Zhang, Zhongyue, et al.
Published: (2025)

ProxelGen: Generating Proteins as 3D Densities
by: Faltings, Felix, et al.
Published: (2025)

Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction
by: Zia, Mushal, et al.
Published: (2024)

Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
by: Liu, Shiyi, et al.
Published: (2025)

ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024)

Deep Learning for Protein Complex Prediction and Design
by: Xie, Ziwei
Published: (2026)

DL4Proteins Jupyter Notebooks Teach how to use Artificial Intelligence for Biomolecular Structure Prediction and Design
by: Chungyoun, Michael, et al.
Published: (2025)

Single-Sequence-Based Protein Secondary Structure Prediction using One-Hot and Chemical Encodings of Amino Acids
by: Trinh, Hoa, et al.
Published: (2024)

Fold-switching Proteins
by: Chakravarty, Devlina, et al.
Published: (2025)

Steering Protein Family Design through Profile Bayesian Flow
by: Gong, Jingjing, et al.
Published: (2025)

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction
by: Alsamkary, Hazem, et al.
Published: (2025)

Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions
by: Sun, Rui, et al.
Published: (2024)