Cover Image

Learning residue level protein dynamics with multiscale Gaussians

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Bafna, Mihir, Jing, Bowen, Berger, Bonnie
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms
by: Jing, Bowen, et al.
Published: (2023)

AlphaFold Meets Flow Matching for Generating Protein Ensembles
by: Jing, Bowen, et al.
Published: (2024)

Generative Modeling of Molecular Dynamics Trajectories
by: Jing, Bowen, et al.
Published: (2024)

AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles
by: Jing, Bowen, et al.
Published: (2025)

Dirichlet Flow Matching with Applications to DNA Sequence Design
by: Stark, Hannes, et al.
Published: (2024)

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins
by: Jing, Bowen, et al.
Published: (2026)

Towards protein folding pathways by reconstructing protein residue networks with a policy-driven model
by: Khor, Susan
Published: (2026)

Identifying critical residues of a protein using meaningfully-thresholded Random Geometric Graphs
by: Zhang, Chuqiao, et al.
Published: (2025)

Representation choice shapes the interpretation of protein conformational dynamics
by: Giottonini, Axel, et al.
Published: (2026)

On fine-tuning Boltz-2 for protein-protein affinity prediction
by: King, James, et al.
Published: (2025)

Sequence-based protein-protein interaction prediction and its applications in drug discovery
by: Charih, François, et al.
Published: (2025)

One protein is all you need
by: Bushuiev, Anton, et al.
Published: (2024)

Evaluating representation learning on the protein structure universe
by: Jamasb, Arian R., et al.
Published: (2024)

Assessing interaction recovery of predicted protein-ligand poses
by: Errington, David, et al.
Published: (2024)

Kermut: Composite kernel regression for protein variant effects
by: Groth, Peter Mørch, et al.
Published: (2024)

Predicting mutational effects on protein binding from folding energy
by: Deng, Arthur, et al.
Published: (2025)

Inference-time optimization for experiment-grounded protein ensemble generation
by: Maddipatla, Advaith, et al.
Published: (2026)

Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data
by: Raghu, Rishwanth, et al.
Published: (2025)

ProteinGuide: On-the-fly property guidance for protein sequence generative models
by: Xiong, Junhao, et al.
Published: (2025)

Mask prior-guided denoising diffusion improves inverse protein folding
by: Bai, Peizhen, et al.
Published: (2024)

MotifBench: A standardized protein design benchmark for motif-scaffolding problems
by: Zheng, Zhuoqi, et al.
Published: (2025)

A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
by: Didi, Kieran, et al.
Published: (2023)

Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems
by: Worah, Pratik, et al.
Published: (2026)

DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction
by: Kotowski, Krzysztof, et al.
Published: (2024)

On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs
by: Young, James Matthew, et al.
Published: (2024)

ProtFAD: Introducing function-aware domains as implicit modality towards protein function prediction
by: Wang, Mingqing, et al.
Published: (2024)

Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids
by: Ferraz, Lucas, et al.
Published: (2026)

Transformer-based toxin-protein interaction analysis prioritizes airborne particulate matter components with potential adverse health effects
by: Zhu, Yan, et al.
Published: (2024)

MolGraph-xLSTM: A graph-based dual-level xLSTM framework with multi-head mixture-of-experts for enhanced molecular representation and interpretability
by: Sun, Yan, et al.
Published: (2025)

Multi-level Interaction Modeling for Protein Mutational Effect Prediction
by: Mo, Yuanle, et al.
Published: (2024)

SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction
by: Huang, Yanwen, et al.
Published: (2024)

FoldToken2: Learning compact, invariant and generative protein structure language
by: Gao, Zhangyang, et al.
Published: (2024)

AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation
by: Zhu, Wenyu, et al.
Published: (2025)

Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion
by: Gao, Bowen, et al.
Published: (2024)

From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics
by: Gao, Bowen, et al.
Published: (2024)

Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processing
by: V, Shreyas, et al.
Published: (2024)

Coder as Editor: Code-driven Interpretable Molecular Optimization
by: Zhu, Wenyu, et al.
Published: (2025)

ENSEMBITS: an alphabet of protein conformational ensembles
by: Shi, Kaiwen, et al.
Published: (2026)

SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision
by: Zheng, Kangjie, et al.
Published: (2024)

ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024)