Multi-Scale Temporal Flows for Peptide Trajectory Generation

arXiv:2610.01086 · q-bio.BM, q-bio.QM · Submitted 2026-10-01 · Read on arXiv

q-bio.BM, q-bio.QM

Submitted: 2026-10-01

Updated: 2026-10-01

Terminology

• Benchmark — 12× in this paper · explained in 2 episodes
• Ablation — 7× in this paper · explained in 1 episode
• Adaptive Physical-Time Embedding — 6× in this paper
• Fidelity — 4× in this paper · explained in 2 episodes
• Generative Model — 4× in this paper · explained in 2 episodes
• Core — 3× in this paper · explained in 2 episodes
• Flow Matching — 3× in this paper · explained in 8 episodes
• Generative Models — 3× in this paper · explained in 2 episodes
• Diffusion Model — 2× in this paper · explained in 8 episodes
• Embeddings — 2× in this paper · explained in 2 episodes
• Generative Modeling — 2× in this paper · explained in 3 episodes
• Ablation study — 1× in this paper · explained in 1 episode
• Adaptation — 1× in this paper · explained in 1 episode
• Fine-Tuning — 1× in this paper · explained in 5 episodes
• Latent Dynamics — 1× in this paper · explained in 2 episodes
• Model-Agnostic — 1× in this paper · explained in 2 episodes
• Normalizing Flow — 1× in this paper · explained in 3 episodes
• Normalizing Flows — 1× in this paper · explained in 4 episodes
• Robustness — 1× in this paper · explained in 5 episodes
• Structural Constraints — 1× in this paper · explained in 2 episodes
• Transformer — 1× in this paper · explained in 2 episodes

Sources

• EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
• Accurate and Efficient Structural Ensemble Generation of Macrocyclic Peptides using Internal Coordinate Diffusion
• Time2Vec: Learning a Vector Representation of Time
• Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
• Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics
• MuCO: Generative Peptide Cyclization Empowered by Multi-stage Conformation Optimization
• Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides

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• p2smi: A Python Toolkit for Peptide FASTA-to-SMILES Conversion and Molecular Property Analysis
• UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions
• Co-folding with a Soup of Representations
• Non-Markovain Quantum State Diffusion for the Tunneling in SARS-COVID-19 virus