Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Weitzman, Ruben, Groth, Peter Mørch, Van Niekerk, Lood, Otani, Aoi, Gal, Yarin, Marks, Debora, Notin, Pascal
Format:	Preprint
Published:	2025
Subjects:	Quantitative Methods Machine Learning Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Pareto-Optimal Offline Reinforcement Learning via Smooth Tchebysheff Scalarization
by: Bhatnagar, Aadyot, et al.
Published: (2026)

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

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

Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
by: Teufel, Felix, et al.
Published: (2025)

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

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

End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform
by: Wu, Yongxian, et al.
Published: (2024)

Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction
by: Yin, Song, et al.
Published: (2023)

Predicting Protein-Nucleic Acid Flexibility Using Persistent Sheaf Laplacians
by: Hayes, Nicole, et al.
Published: (2025)

Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
by: Reilly, Charles B
Published: (2026)

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

Protein-Mamba: Biological Mamba Models for Protein Function Prediction
by: Xu, Bohao, et al.
Published: (2024)

Persistent Sheaf Laplacian Analysis of Protein Flexibility
by: Hayes, Nicole, et al.
Published: (2025)

Impact of Force Field Polarization on Correlated Motions of Proteins
by: Milinski, Ana, et al.
Published: (2025)

Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
by: Lim, Hocheol, et al.
Published: (2025)

ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution
by: Cheng, Lixue, et al.
Published: (2022)

UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection
by: Fan, Jigang, et al.
Published: (2025)

Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
by: Ghafouri, Hamidreza, et al.
Published: (2025)

VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels
by: Wang, Rui, et al.
Published: (2026)

LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
by: Phan, An, et al.
Published: (2026)

Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold
by: Chib, Garima, et al.
Published: (2025)

Protein folding classes -- High-dimensional geometry of amino acid composition space revisited
by: Mao, Boryeu
Published: (2025)

Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning
by: Clark, Joseph D., et al.
Published: (2024)

Explainable Machine Learning and Deep Learning Models for Predicting TAS2R-Bitter Molecule Interactions
by: Ferri, Francesco, et al.
Published: (2024)

Protein Fold Classification at Scale: Benchmarking and Pretraining
by: Chen, Dexiong, et al.
Published: (2026)

Endowing Protein Language Models with Structural Knowledge
by: Chen, Dexiong, et al.
Published: (2024)

Conditioning Protein Generation via Hopfield Pattern Multiplicity
by: Varner, Jeffrey D.
Published: (2026)

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

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
by: Lu, Jiarui, et al.
Published: (2024)

Differentiable Folding for Nearest Neighbor Model Optimization
by: Krueger, Ryan K., et al.
Published: (2025)

Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives
by: Liu, Xiaokun, et al.
Published: (2025)

Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs
by: Chatzianastasis, Michail, et al.
Published: (2024)

A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics
by: Liu, Shengchao, et al.
Published: (2024)

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
by: Lu, Jiarui, et al.
Published: (2023)

GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
by: Lindsey, Michael
Published: (2026)

Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
by: Baillif, Benoit, et al.
Published: (2024)

Canonicalization of the E value from BLAST similarity search -- dissimilarity measure and distance function for a metric space of protein sequences
by: Mao, Boryeu
Published: (2025)

AntiFold: Improved antibody structure-based design using inverse folding
by: Høie, Magnus Haraldson, et al.
Published: (2024)

HelixVS: Deep Learning-Enhanced Structure-Based Platform for Screening and Design
by: Zhang, Shanzhuo, et al.
Published: (2025)

EscalNet: Learn isotropic representation space for biomolecular dynamics based on effective energy
by: Zuo, Guanghong
Published: (2025)