Evaluating protein binding interfaces with PUMBA
Fuente:
arXiv
Saved in:
| Main Authors: | Shirali, Azam, Narasimhan, Giri |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Improved prediction of ligand-protein binding affinities by meta-modeling
by: Lee, Ho-Joon, et al.
Published: (2023)
by: Lee, Ho-Joon, et al.
Published: (2023)
Edge-aware GAT-based protein binding site prediction
by: Yang, Weisen, et al.
Published: (2026)
by: Yang, Weisen, et al.
Published: (2026)
ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning
by: Zeng, Wenwu, et al.
Published: (2023)
by: Zeng, Wenwu, et al.
Published: (2023)
Blood Glucose Level Prediction in Type 1 Diabetes Using Machine Learning
by: Chu, Soon Jynn, et al.
Published: (2025)
by: Chu, Soon Jynn, et al.
Published: (2025)
Why risk matters for protein binder design
by: Cotet, Tudor-Stefan, et al.
Published: (2025)
by: Cotet, Tudor-Stefan, et al.
Published: (2025)
Deep learning-guided evolutionary optimization for protein design
by: Hartman, Erik, et al.
Published: (2026)
by: Hartman, Erik, et al.
Published: (2026)
Controllable protein design with particle-based Feynman-Kac steering
by: Hartman, Erik, et al.
Published: (2025)
by: Hartman, Erik, et al.
Published: (2025)
Understanding protein function with a multimodal retrieval-augmented foundation model
by: Truong Jr, Timothy Fei, et al.
Published: (2025)
by: Truong Jr, Timothy Fei, et al.
Published: (2025)
PoET: A generative model of protein families as sequences-of-sequences
by: Truong Jr, Timothy F., et al.
Published: (2023)
by: Truong Jr, Timothy F., et al.
Published: (2023)
Linguistically inspired roadmap for building biologically reliable protein language models
by: Vu, Mai Ha, et al.
Published: (2022)
by: Vu, Mai Ha, et al.
Published: (2022)
How to make the most of your masked language model for protein engineering
by: McCarter, Calvin, et al.
Published: (2026)
by: McCarter, Calvin, et al.
Published: (2026)
PTransIPs: Identification of phosphorylation sites enhanced by protein PLM embeddings
by: Xu, Ziyang, et al.
Published: (2023)
by: Xu, Ziyang, et al.
Published: (2023)
Mixing Vector Model for Copolymer Inference via Mixed Integer Linear Programming
by: Zhu, Jianshen, et al.
Published: (2026)
by: Zhu, Jianshen, et al.
Published: (2026)
GCBLANE: A graph-enhanced convolutional BiLSTM attention network for improved transcription factor binding site prediction
by: Ferrao, Jonas Chris, et al.
Published: (2025)
by: Ferrao, Jonas Chris, et al.
Published: (2025)
Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability
by: Rodrigues, Ana F., et al.
Published: (2026)
by: Rodrigues, Ana F., et al.
Published: (2026)
Exploring zero-shot structure-based protein fitness prediction
by: Sharma, Arnav, et al.
Published: (2025)
by: Sharma, Arnav, et al.
Published: (2025)
Generative power of a protein language model trained on multiple sequence alignments
by: Sgarbossa, Damiano, et al.
Published: (2022)
by: Sgarbossa, Damiano, et al.
Published: (2022)
SeFEF: A Seizure Forecasting Evaluation Framework
by: Carmo, Ana Sofia, et al.
Published: (2025)
by: Carmo, Ana Sofia, et al.
Published: (2025)
Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Prediction
by: Liu, Songtao, et al.
Published: (2024)
by: Liu, Songtao, et al.
Published: (2024)
From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering
by: Li, Wen-ran, et al.
Published: (2025)
by: Li, Wen-ran, et al.
Published: (2025)
Compressing Biology: Evaluating the Stable Diffusion VAE for Phenotypic Drug Discovery
by: Cropsal, Télio, et al.
Published: (2025)
by: Cropsal, Télio, et al.
Published: (2025)
Driving Accurate Allergen Prediction with Protein Language Models and Generalization-Focused Evaluation
by: Wong, Brian Shing-Hei, et al.
Published: (2025)
by: Wong, Brian Shing-Hei, et al.
Published: (2025)
Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks
by: Chen, Angelica, et al.
Published: (2024)
by: Chen, Angelica, et al.
Published: (2024)
Evaluation of Country Dietary Habits Using Machine Learning Techniques in Relation to Deaths from COVID-19
by: García-Ordás, María Teresa, et al.
Published: (2024)
by: García-Ordás, María Teresa, et al.
Published: (2024)
Toward Scalable Early Cancer Detection: Evaluating EHR-Based Predictive Models Against Traditional Screening Criteria
by: Park, Jiheum, et al.
Published: (2025)
by: Park, Jiheum, et al.
Published: (2025)
LAMP-PRo: Label-aware Attention for Multi-label Prediction of DNA- and RNA-binding Proteins using Protein Language Models
by: Ghosh, Nimisha, et al.
Published: (2025)
by: Ghosh, Nimisha, et al.
Published: (2025)
ReFine: Boosting Time Series Prediction of Extreme Events by Reweighting and Fine-tuning
by: Shi, Jimeng, et al.
Published: (2024)
by: Shi, Jimeng, et al.
Published: (2024)
Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling
by: Wu, Fang, et al.
Published: (2026)
by: Wu, Fang, et al.
Published: (2026)
Generative modeling of protein ensembles guided by crystallographic electron densities
by: Maddipatla, Sai Advaith, et al.
Published: (2024)
by: Maddipatla, Sai Advaith, et al.
Published: (2024)
Protein binding affinity prediction under multiple substitutions applying eGNNs on Residue and Atomic graphs combined with Language model information: eGRAL
by: Fiorellini-Bernardis, Arturo, et al.
Published: (2024)
by: Fiorellini-Bernardis, Arturo, et al.
Published: (2024)
Loop-Diffusion: an equivariant diffusion model for designing and scoring protein loops
by: Borisiak, Kevin, et al.
Published: (2024)
by: Borisiak, Kevin, et al.
Published: (2024)
PPI-Net connects molecular protein interactions to functional processes in disease
by: Higgins, Kyle, et al.
Published: (2026)
by: Higgins, Kyle, et al.
Published: (2026)
PatchProt: Hydrophobic patch prediction using protein foundation models
by: Gogishvili, Dea, et al.
Published: (2024)
by: Gogishvili, Dea, et al.
Published: (2024)
Zepyros: A webserver to evaluate the shape complementarity of protein-protein interfaces
by: Miotto, Mattia, et al.
Published: (2024)
by: Miotto, Mattia, et al.
Published: (2024)
Expanding functional protein sequence space using high entropy generative models
by: Netti, Roberto, et al.
Published: (2026)
by: Netti, Roberto, et al.
Published: (2026)
Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design
by: Zheng, Jiangbin, et al.
Published: (2024)
by: Zheng, Jiangbin, et al.
Published: (2024)
Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences
by: Jiang, Shiyu, et al.
Published: (2025)
by: Jiang, Shiyu, et al.
Published: (2025)
GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration
by: Li, Ziwen, et al.
Published: (2025)
by: Li, Ziwen, et al.
Published: (2025)
Explainable Deep Learning Framework for SERS Bio-quantification
by: Zaki, Jihan K., et al.
Published: (2024)
by: Zaki, Jihan K., et al.
Published: (2024)
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024)
by: Viswanath, Siddharth, et al.
Published: (2024)
Similar Items
-
Improved prediction of ligand-protein binding affinities by meta-modeling
by: Lee, Ho-Joon, et al.
Published: (2023) -
Edge-aware GAT-based protein binding site prediction
by: Yang, Weisen, et al.
Published: (2026) -
ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning
by: Zeng, Wenwu, et al.
Published: (2023) -
Blood Glucose Level Prediction in Type 1 Diabetes Using Machine Learning
by: Chu, Soon Jynn, et al.
Published: (2025) -
Why risk matters for protein binder design
by: Cotet, Tudor-Stefan, et al.
Published: (2025)