Best Practices for Machine Learning-Assisted Protein Engineering
Fuente:
arXiv
Saved in:
| Main Authors: | Herrera-Rocha, Fabio, Medina-Ortiz, David, Mauz, Fabian, Pleiss, Juergen, Davari, Mehdi D. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
by: Zhang, Yanzi, et al.
Published: (2025)
by: Zhang, Yanzi, et al.
Published: (2025)
Decoding Polyphenol-Protein Interactions with Deep Learning: From Molecular Mechanisms to Food Applications
by: Liu, Qiang, et al.
Published: (2025)
by: Liu, Qiang, 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)
by: Zia, Mushal, et al.
Published: (2024)
Deep Learning of Proteins with Local and Global Regions of Disorder
by: Zhang, Oufan, et al.
Published: (2025)
by: Zhang, Oufan, et al.
Published: (2025)
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
by: Majewski, Maciej, et al.
Published: (2022)
by: Majewski, Maciej, et al.
Published: (2022)
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
by: Yalabadi, Ali Khodabandeh, et al.
Published: (2025)
by: Yalabadi, Ali Khodabandeh, et al.
Published: (2025)
Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction
by: Yin, Song, et al.
Published: (2023)
by: Yin, Song, et al.
Published: (2023)
Guiding Generative Protein Language Models with Reinforcement Learning
by: Stocco, Filippo, et al.
Published: (2024)
by: Stocco, Filippo, et al.
Published: (2024)
Advances of Deep Learning in Protein Science: A Comprehensive Survey
by: Hu, Bozhen, et al.
Published: (2024)
by: Hu, Bozhen, et al.
Published: (2024)
Diffusion Sequence Models for Enhanced Protein Representation and Generation
by: Hallee, Logan, et al.
Published: (2025)
by: Hallee, Logan, et al.
Published: (2025)
Protein FID: Improved Evaluation of Protein Structure Generative Models
by: Faltings, Felix, et al.
Published: (2025)
by: Faltings, Felix, et al.
Published: (2025)
Fold-switching Proteins
by: Chakravarty, Devlina, et al.
Published: (2025)
by: Chakravarty, Devlina, et al.
Published: (2025)
AlphaFold2 for protein structure prediction: Best practices and critical analyses
by: Radjasandirane, Ragousandirane, et al.
Published: (2024)
by: Radjasandirane, Ragousandirane, et al.
Published: (2024)
Decoding How Proteins Fold
by: Vila, Jorge
Published: (2025)
by: Vila, Jorge
Published: (2025)
PLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction
by: Xu, Xingjian, et al.
Published: (2024)
by: Xu, Xingjian, et al.
Published: (2024)
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability
by: Kyro, Gregory W., et al.
Published: (2024)
by: Kyro, Gregory W., et al.
Published: (2024)
SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins
by: Jing, Bowen, et al.
Published: (2026)
by: Jing, Bowen, et al.
Published: (2026)
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)
by: Lim, Hocheol, et al.
Published: (2025)
Toward the Explainability of Protein Language Models
by: Hunklinger, Andrea, et al.
Published: (2025)
by: Hunklinger, Andrea, et al.
Published: (2025)
Topological Enhancement of Protein Kinetic Stability
by: Especial, João NC, et al.
Published: (2026)
by: Especial, João NC, et al.
Published: (2026)
Protein Evolution as a Complex System
by: Gall, Barnabas, et al.
Published: (2024)
by: Gall, Barnabas, et al.
Published: (2024)
Atom-level Protein Representation Learning Improves Protein Structure Prediction
by: Kim, Taewon, et al.
Published: (2026)
by: Kim, Taewon, et al.
Published: (2026)
Implicitly and Differentiably Representing Protein Surfaces and Interfaces
by: Scott, Cory B., et al.
Published: (2025)
by: Scott, Cory B., et al.
Published: (2025)
Probing the Dark Energy in the Functional Protein Universe
by: Galpern, Ezequiel A., et al.
Published: (2025)
by: Galpern, Ezequiel A., et al.
Published: (2025)
A Comprehensive Review of Protein Language Models
by: Wang, Lei, et al.
Published: (2025)
by: Wang, Lei, et al.
Published: (2025)
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering
by: Shen, Yiqing, et al.
Published: (2024)
by: Shen, Yiqing, et al.
Published: (2024)
Discrimination vs. Generation: The Machine Learning Dichotomy for Dopaminergic Hit Discovery
by: Sobodu, Temitope, et al.
Published: (2024)
by: Sobodu, Temitope, et al.
Published: (2024)
Adaptive Protein Tokenization
by: Dilip, Rohit, et al.
Published: (2026)
by: Dilip, Rohit, et al.
Published: (2026)
Into the Unknown: From Structure to Disorder in Protein Function Prediction
by: Kolarić, Đesika, et al.
Published: (2025)
by: Kolarić, Đesika, et al.
Published: (2025)
Atomic Density Distributions in Proteins: Structural and Functional Implications
by: Touliopoulos, Sotirios, et al.
Published: (2025)
by: Touliopoulos, Sotirios, et al.
Published: (2025)
Hermes: Large DEL Datasets Train Generalizable Protein-Ligand Binding Prediction Models
by: Kleinsasser, Maxwell, et al.
Published: (2026)
by: Kleinsasser, Maxwell, et al.
Published: (2026)
ProtScan: Modeling and Prediction of RNA-Protein Interactions
by: Corrado, Gianluca, et al.
Published: (2024)
by: Corrado, Gianluca, et al.
Published: (2024)
Design of Ligand-Binding Proteins with Atomic Flow Matching
by: Liu, Junqi, et al.
Published: (2024)
by: Liu, Junqi, et al.
Published: (2024)
A New Route for the Determination of Protein Structure and Function
by: Mejias, S. H., et al.
Published: (2024)
by: Mejias, S. H., et al.
Published: (2024)
Decision Tree for Protein Biomarker Selection for Clinical Applications
by: Waury, Katharina
Published: (2023)
by: Waury, Katharina
Published: (2023)
Latent-X: An Atom-level Frontier Model for De Novo Protein Binder Design
by: Latent Labs Team, et al.
Published: (2025)
by: Latent Labs Team, et al.
Published: (2025)
Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
by: Liu, Shiyi, et al.
Published: (2025)
by: Liu, Shiyi, et al.
Published: (2025)
A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design
by: Dai, Weihang
Published: (2025)
by: Dai, Weihang
Published: (2025)
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024)
by: Halfon, Matan, et al.
Published: (2024)
Steering Generative Models for Protein Design: Aligning and Conditioning Strategies
by: Stocco, Filippo, et al.
Published: (2025)
by: Stocco, Filippo, et al.
Published: (2025)
Similar Items
-
Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
by: Zhang, Yanzi, et al.
Published: (2025) -
Decoding Polyphenol-Protein Interactions with Deep Learning: From Molecular Mechanisms to Food Applications
by: Liu, Qiang, 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) -
Deep Learning of Proteins with Local and Global Regions of Disorder
by: Zhang, Oufan, et al.
Published: (2025) -
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
by: Majewski, Maciej, et al.
Published: (2022)