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Applications · Chemistry and Drug Discovery

Juno Nam, Bálint Máté, Artur Toshev, Manasa Kaniselvan, Rafael Gomez-Bombarelli, Ricky T. Q. Chen, Brandon Wood, Guan-Horng Liu, Benjamin Miller

Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular dynamics and miss thermodynamically relevant modes. Inspired by enhanced sampling, we encourage exploration by introducing a sequential bias along bespoke, information-rich, low-dimensional projections of atomic coordinates known as collective variables (CVs). We introduce a repulsive potential centered on the CVs from recent samples, which pushes future samples towards novel CV regions and effectively increases the temperature in the projected space. Our resulting method improves efficiency, mode discovery, enables the estimation of free energy differences, and retains independent sampling from the approximate Boltzmann distribution via reweighting by the bias. On standard peptide conformational sampling benchmarks, the method recovers diverse conformational states and accurate free energy profiles. We are the first to demonstrate reactive sampling using a diffusion-based sampler, capturing bond breaking and formation with universal interatomic potentials at near-first-principles accuracy. The approach resolves reactive energy landscapes at a fraction of the wall-clock time of standard sampling methods, advancing diffusion-based sampling towards practical use in molecular sciences.

Applications · Chemistry and Drug Discovery

Zhe Zhang, Yuanning Feng, Yuxuan Song, Keyue Qiu, Hao Zhou, Wei-Ying Ma

AlphaFold3 introduces a diffusion-based architecture that elevates protein structure prediction to all-atom resolution with improved accuracy. This state-of-the-art performance has established AlphaFold3 as a foundation model for diverse generation and design tasks. However, its iterative design substantially increases inference time, limiting practical deployment in downstream settings such as virtual screening and protein design. We propose DCFold, a single-step generative model that attains AlphaFold3-level accuracy. Our Dual Consistency training framework, which incorporates a novel Temporal Geodesic Matching (TGM) scheduler, enables DCFold to achieve a 15× acceleration in inference while maintaining predictive fidelity. We validate its effectiveness across both structure prediction and binder design benchmarks.

Applications · Chemistry and Drug Discovery

Yanru Qu, Yijie Zhang, Wenjuan Tan, Xiangzhe Kong, Xiangxin Zhou, Chaoran Cheng, Mathieu Blanchette, Jiaxuan You, Ge Liu

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking, which occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, individual atoms cannot express stereochemistry, lone pairs, conjugation, and other complex features. Fragment-based methods (e.g., principal subgraph or functional group libraries) fail to preserve essential information such as chirality, aromatic bond integrity, and ionic states. This work addresses these limitations from two aspects. (i) OverlapBPE tokenization. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) h- MINT model. We develop a hierarchical molecular interaction network capable of jointly modeling drug–target interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to- many atom–fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.

Applications · Chemistry and Drug Discovery

Kevin Tirta Wijaya, Bing Hu, Hans-Peter Seidel, Wojciech Matusik, Vahid Babaei

Accurate regression models are essential for scientific discovery, yet high-quality numeric labels are scarce and expensive. In contrast, rankings (especially pairwise) are easier to obtain from domain experts or artificial intelligence judges. We introduce RankRefine++, a novel plug-and-play method that improves a base regressor's prediction for a query by leveraging pairwise rankings between the query and reference items with known labels. RankRefine++ performs a Bayesian update that combines a Gaussian likelihood from the regressor and the Bradley-Terry likelihood from the ranker. This yields a strictly log-concave posterior with a unique maximum likelihood solution and fast Newton updates. We show that prior state-of-the-art is a special case of our framework, and we identify a fundamental failure mode: Bradley-Terry likelihoods suffer from scale mismatch and curvature dominance when the number of reference items is large, which can degrade performance. From this analysis, we derive a calibration method to adjust the information originating from the expert rankings. RankRefine++ shows a stunning 97.65\% median improvement across 12 datasets over previous state-of-the-art method using a realistically-accurate ranker, and runs efficiently on a consumer-grade CPU.

Applications · Chemistry and Drug Discovery

Luke Thompson, Davy Guan, Slade Matthews, Dai Shi, Junbin Gao, Andi Han

Molecular dynamics (MD) simulations underpin modern computational drug discovery, materials science, and biochemistry. Recent machine learning models provide high-fidelity MD predictions without the need for repeated quantum-mechanical force calculations, enabling significant speedups over conventional pipelines. Yet many such methods typically enforce strict equivariance and rely on sequential rollouts, thus limiting their flexibility and simulation efficiency. They are also commonly single-task, trained on individual molecules and fixed time frames, which restricts generalization to unseen compounds and extended timesteps. To address these issues, we propose Atomistic Transformer Operator for Molecules (ATOM), a pretrained transformer neural operator for multi-task molecular dynamics. ATOM adopts a quasi-equivariant design that does not require an explicit molecular graph and employs a temporal attention mechanism to enable accurate, parallel decoding of multiple future states. To support operator pretraining across chemicals and timescales, we curate TG80, a large, diverse, and numerically stable MD dataset with over 2.5 million femtoseconds of trajectories across 80 compounds. ATOM achieves state-of-the-art performance on established single-task benchmarks, such as MD17, RMD17, and MD22. After multi-task pretraining on TG80, ATOM shows exceptional zero-shot and robust generalization to unseen molecules across varying time horizons. We believe ATOM represents a significant step toward accurate, efficient, and transferable molecular dynamics models.

Applications · Chemistry and Drug Discovery

Gang Liu, Jie Chen, Yihan Zhu, Michael Sun, Tengfei Luo, Nitesh Chawla, Meng Jiang

In-context learning lets large models adapt to new tasks from a few demonstrations, but it has shown limited success in molecular design, where labeled data are scarce and properties span millions of biological assays and material measurements. We introduce demonstration-conditioned diffusion models (DemoDiff), which define task contexts through molecule–score examples instead of texts. These demonstrations guide a denoising Transformer to generate molecules aligned with target properties. For scalable pretraining, we develop a new molecular tokenizer with Node Pair Encoding that represents molecules at the motif level, requiring 5.5$\times$ fewer nodes. We pretrain a 0.7B parameter model on datasets covering drugs and materials. Across 33 design tasks in six categories, DemoDiff matches or surpasses language models 100–1000$\times$ larger and achieves an average rank of 4.10 compared to 6.56–17.95 for 19 baselines. These results position DemoDiff as a molecular foundation model for in-context molecular design.

Applications · Chemistry and Drug Discovery

Carl Edwards, Chi Han, Gawon Lee, Thao Nguyen, Sara Szymkuć, Chetan Prasad, Bowen Jin, Jiawei Han, Ying Diao, Ge Liu 等

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. Experiments on 430 FDA-approved drugs showed that mCLM is capable of significantly improving chemical functions critical to determining drug potentials. mCLM, with only 3B parameters, also achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials (“fallen angels”).

Applications · Chemistry and Drug Discovery

Haochen Wang, Qianyi Wang, Rui Ma, Jiawei Guan, weikun wu, haobo wang, Jiayi Dou

Small-molecule ligands extend protein functionality beyond natural amino acids, enabling sophisticated processes like catalysis, signal transduction, and light harvesting. However, designing proteins with high affinity and selectivity for arbitrary ligands remains a major challenge. We present Pallatom-Ligand, a diffusion model that performs end-to-end generation of ligand-binding proteins at atomic resolution. By directly learning the joint distribution of all atoms in the protein–ligand complexes, Pallatom-Ligand delivers state-of-the-art performance, achieving the highest *in silico* success rates in a comprehensive benchmark. In addition, Pallatom-Ligand's novel conditioning framework enables programmable control over global protein fold and atomic-level ligand solvent accessibility. With these capabilities, Pallatom-Ligand opens new opportunities for exploring the protein function space, advancing both generative modeling and computational protein engineering.

Applications · Chemistry and Drug Discovery

Yunfan Liu, Lirong Wu, Zhifeng Gao, Yufei Huang, Cheng Tan, Haitao Lin, Zicheng Liu, Changxi Chi, Chang Yu, Stan Z Li

Designing 3D ligands that bind to a given protein pocket with high affinity is a fundamental task in Structure-Based Drug Design (SBDD). However, the lack of synthesizability of 3D ligands has been hindering progress toward experimental validation; moreover, computationally evaluating synthesizability is a non-trivial task. In this paper, we first benchmark eight classical synthesizability metrics across 11 SBDD methods. The comparison reveals significant inconsistencies between these metrics, making them impractical and inaccurate criteria for guiding SBDD methods toward synthesizable drug design. Therefore, we propose a simple yet effective SE(3)-invariant \textit{\underline{SYN}thesizability \underline{C}lassifier} (SYNC) to enable better synthesizability estimation in SBDD, which demonstrates superior generalizability and speed compared to existing metrics on five curated datasets. Finally, with SYNC as a plug-and-play module, we establish a synthesizability classifier-driven SBDD paradigm through guided diffusion and Direct Preference Optimization, where highly synthesizable molecules are directly generated without compromising binding affinity. Extensive experiments also demonstrate the effectiveness of SYNC and the advantage of our paradigm in synthesizable SBDD. Code is available at \url{https://github.com/XYxiyang/SYNC}.

Applications · Chemistry and Drug Discovery

Ngoc-Quang Nguyen, Jaeyoon Jung, Seijung Kim, Sunkyu Kim, Jaewoo Kang

Peptides, short chains of amino acids capable of high-specificity protein binding, represent a powerful class of therapeutics. While deep generative models have shown promise for peptide design, existing approaches are often structure-centric and therefore generate sequences and structures in a decoupled manner, failing to ensure that designs are simultaneously physically stable, evolutionarily plausible, and internally coherent. To overcome this limitation, we introduce \textbf{PepTri}, a novel diffusion framework that addresses this by jointly generating peptide sequences and 3D structures within a unified, SE(3)-equivariant latent space. Our proposed model integrates three complementary guidance signals during the generative process: (i) physics-informed guidance via differentiable molecular mechanics to ensure structural stability and realism; (ii) evolutionary guidance to bias sequences toward conserved, functional motifs; and (iii) mutual information guidance to explicitly maximize sequence-structure coherence. This tri-guided approach ensures the generative process is steered by biophysical laws, biological priors, and information-theoretic alignment in tandem. Extensive evaluations on challenging peptide-protein design benchmarks, cross-domain (PepBench, LNR) and in-domain (PepBDB), demonstrate that PepTri substantially outperforms strong baselines, achieving state-of-the-art results in binding affinity, structural accuracy, and design diversity. Our results establish that integrating these complementary signals directly into the denoising process is crucial for generating viable, high-quality peptide medicines. PepTri is available at: https://github.com/aigensciences/PepTri

Applications · Chemistry and Drug Discovery

Michael Sun, Weize Yuan, Gang Liu, Wojciech Matusik, Marinka Zitnik

Protein structure is central to biological function, and enabling multimodal protein models requires joint reasoning over sequence, structure, and function. A key barrier is the lack of principled protein structure tokenizers (PSTs): existing approaches fix token size or rely on continuous vector codebooks, limiting interpretability, multi-scale control, and transfer across architectures. We introduce GeoBPE, a geometry-grounded PST that transforms continuous, noisy, multi-scale backbone conformations into discrete ``sentences'' of geometry while enforcing global constraints. Analogous to byte-pair encoding, GeoBPE generates a hierarchical vocabulary of geometric primitives by iteratively (i) clustering Geo-Pair occurrences with k-medoids to yield a resolution-controllable vocabulary; (ii) quantizing each Geo-Pair to its closest medoid prototype; and (iii) reducing drift through differentiable inverse kinematics that optimizes boundary glue angles under an $\mathrm{SE}(3)$ end-frame loss. GeoBPE offers compression ($>$10× reduction in bits-per-residue at similar distortion rate), data efficiency ($>$10× less training data), and generalization (maintains test/train distortion ratio of $1.0-1.1$). It is architecture-agnostic: (a) its hierarchical vocabulary provides a strong inductive bias for coarsening residue-level embeddings from large PLMs into motif- and protein-level representations, consistently outperforming leading PSTs across $12$ tasks and $24$ test splits; (b) paired with a transformer, GeoBPE supports unconditional backbone generation via language modeling; and (c) tokens align with CATH functional families and support expert-interpretable case studies, offering functional meaning absent in prior PSTs.

Applications · Chemistry and Drug Discovery

Qingyu Wang, Xinyuan Cai, Xiang Cheng, YuZhe Gao, Bo XU

In organic reaction prediction, many recent approaches ranging from traditional task-specific models to Large Language Models (LLMs), have demonstrated notable success. However, these methods are inherently data-driven, exhibit constrained interpretability, and have hit fundamental performance bottlenecks. To overcome these limitations, we present Reaction-Thinker, a hybrid, knowledge‑and-data‑driven system that is enhanced by Retrieval‑Augmented Generation (RAG) and powered by advanced reasoning, improving both the interpretability of prediction process and the explainability of results. We develop similar-case retrieval database and train a RAG‑based LLM through supervised fine-tuning (SFT) to apply both reaction types and similar reaction cases as knowledge. We also construct a reaction reasoning chain-of-thought (CoT) dataset and train a reasoning-based LLM through SFT, then further optimize it using Group Relative Policy Optimization (GRPO). Experimental results show that our method outperforms all compared LLMs and task-specific models, achieving the highest accuracy (Exact Match) and fingerprint similarity (FTS). Ablation study indicates improvements in relative accuracy of 7.5% and 13.9% for RAG and GRPO, respectively. Further analysis of mispredictions reveals limitations in conventional evaluation metrics, which motivates our proposed benchmarking refinement.

Applications · Chemistry and Drug Discovery

Yuhang Xie, Sinno Jialin Pan

Graph generation plays an important role in various domains such as molecular design, protein prediction, and drug discovery. However, generating graph-structured data poses challenges due to the complex dependencies inherent in graphs, spanning from intricate local substructures to broad global topologies. Although recent advances in graph-generative models have made notable progress, traditional node-level generative paradigms may have difficulty simultaneously capturing the multiscale dependencies in graphs. To address these challenges, we propose a unified latent diffusion model that jointly learns local and global topological information, enabling effective and efficient graph generation. Besides, our approach introduces a dual conditioning mechanism designed to promote dynamic interaction between local and global information, equipping the generative model with global and local awareness to better capture the coupled dependencies within graphs. Our method can largely promote the joint modeling of global and local information and substantially improve the quality of the generated graphs. Extensive experiments consistently demonstrate the effectiveness of our method.

Applications · Chemistry and Drug Discovery

Aniketh Iyengar, Jiaqi Han, Pengwei Sun, Mingjian Jiang, Jianwen Xie, Stefano Ermon

Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling high-dimensional MD distributions. To overcome these challenges, we propose a novel framework that leverages structure pre-training for MD trajectory generation. Specifically, we first train a diffusion-based structure generation model on a large-scale conformer dataset, on top of which we introduce an interpolator module trained on MD trajectory data, designed to enforce temporal consistency among generated structures. Our approach effectively harnesses abundant structural data to mitigate the scarcity of MD trajectory data and effectively decomposes the intricate MD modeling task into two manageable subproblems: structural generation and temporal alignment. We comprehensively evaluate our method on the QM9 and DRUGS small-molecule datasets across unconditional generation, forward simulation, and interpolation tasks, and further extend our framework and analysis to tetrapeptide and protein monomer systems. Experimental results confirm that our approach excels in generating chemically realistic MD trajectories, as evidenced by remarkable improvements of accuracy in geometric, dynamical, and energetic measurements.

Applications · Chemistry and Drug Discovery

Lu Yu, Wei Xiang, Kang Han, Gaowen Liu, Ramana Kompella

A key step in protein optimization is modeling the fitness landscape, which maps proteins to functional assay readouts. Existing methods typically either use property-agnostic likelihoods/embeddings from pretrained protein language models (PLMs) for fitness prediction, or assume independent mutational effects, limiting their ability to capture higher-order interactions. In this work, we introduce RankFlow, a conditional flow framework that refines PLM representations to be a property-aligned distribution via a tailored energy function and captures multi-mutation interactions through learnable embeddings. To align optimization with evaluation protocols, we propose the Rank-Consistent Conditional Flow Loss (RC$^2$), a differentiable ranking objective that enforces the correct order of mutants rather than absolute values, which improves out-of-distribution generalization. Finally, we introduce a Property-guided Steering Gate (PSG) that concentrates learning on positions carrying signals for the target property while suppressing unrelated evolutionary biases. Across the ProteinGym, PEER, and FLIP benchmarks, RankFlow obtains state-of-the-art ranking accuracy and superior generalization performance.

Applications · Chemistry and Drug Discovery

Giacomo Turri, Luigi Bonati, Kai Zhu, massimiliano pontil, Pietro Novelli

We introduce an end-to-end approach to learn the evolution operators of large-scale non-linear dynamical systems, such as those describing complex natural phenomena. Evolution operators are particularly well-suited for analyzing systems that exhibit spatio-temporal patterns and have become a key analytical tool across various scientific communities. As terabyte-scale weather datasets and simulation tools capable of running millions of molecular dynamics steps per day are becoming commodities, our approach provides an effective tool to make sense of them from a data-driven perspective. The core of it lies in a remarkable connection between self-supervised representation learning methods and the recently established learning theory of evolution operators. We deploy our approach across multiple scientific domains: explaining the folding dynamics of small proteins, the binding process of drug-like molecules in host sites, and autonomously finding patterns in climate data. Our code is available open-source at: https://github.com/pietronvll/encoderops.

Applications · Chemistry and Drug Discovery

Andrei Rekesh, Miruna Cretu, Dmytro Shevchuk, Pietro Lio, Robert Batey, Mike Tyers, Michał Koziarski, Chenghao Liu

Ensuring synthesizability in generative small molecule design remains a major challenge. While recent developments in synthesizable molecule generation have demonstrated promising results, these efforts have been largely confined to 2D molecular graph representations, limiting the ability to perform geometry-based conditional generation. In this work, we present SYNCOGEN (Synthesizable Co-Generation), a single framework that combines simultaneous masked graph diffusion and flow matching for synthesizable 3D molecule generation. SYNCOGEN samples from the joint distribution of molecular building blocks, chemical reactions, and atomic coordinates. To train the model, we curated SYNSPACE, a dataset containing over 600K synthesis-aware building block graphs and 3.3M conformers. SYNCOGEN achieves state-of-the-art performance in unconditional small molecule graph and conformer generation, and the model delivers competitive performance in zero-shot molecular linker design and pharmacophore conditioning for protein ligand generation in drug discovery. Overall, this multimodal formulation represents a foundation for future applications enabled by non-autoregressive molecular generation, including analog expansion, lead optimization, and direct structure conditioning.

Applications · Chemistry and Drug Discovery

Yunqing LIU, Yi Zhou, Wenqi Fan

Molecule representation learning is crucial for understanding and predicting molecular properties. However, conventional atom-centric models, which treat chemical bonds merely as pairwise interactions, often overlook complex bond-level phenomena like resonance and stereoselectivity. This oversight limits their predictive accuracy for nuanced chemical behaviors. To address this limitation, we introduce \textbf{DeMol}, a dual-graph framework whose architecture is motivated by a rigorous information-theoretic analysis demonstrating the information gain from a bond-centric perspective. DeMol explicitly models molecules through parallel atom-centric and bond-centric channels. These are synergistically fused by multi-scale Double-Helix Blocks designed to learn intricate atom-atom, atom-bond, and bond-bond interactions. The framework's geometric consistency is further enhanced by a regularization term based on covalent radii to enforce chemically plausible structures. Comprehensive evaluations on diverse benchmarks, including PCQM4Mv2, OC20 IS2RE, QM9, and MoleculeNet, show that DeMol establishes a new state-of-the-art, outperforming existing methods. These results confirm the superiority of explicitly modelling bond information and interactions, paving the way for more robust and accurate molecular machine learning.

Applications · Chemistry and Drug Discovery

Xingyu Su, Xiner Li, Masatoshi Uehara, Sunwoo Kim, Yulai Zhao, Gabriele Scalia, Ehsan Hajiramezanali, Tommaso Biancalani, Degui Zhi, Shuiwang Ji

We address the problem of fine-tuning diffusion models for reward-guided generation in biomolecular design. While diffusion models have proven highly effective in modeling complex, high-dimensional data distributions, real-world applications often demand more than high-fidelity generation, requiring optimization with respect to potentially non-differentiable reward functions such as physics-based simulation or rewards based on scientific knowledge. Although RL methods have been explored to fine-tune diffusion models for such objectives, they often suffer from instability, low sample efficiency, and mode collapse due to their on-policy nature. In this work, we propose an iterative distillation-based fine-tuning framework that enables diffusion models to optimize for arbitrary reward functions. Our method casts the problem as policy distillation: it collects off-policy data during the roll-in phase, simulates reward-based soft-optimal policies during roll-out, and updates the model by minimizing the KL divergence between the simulated soft-optimal policy and the current model policy. Our off-policy formulation, combined with KL divergence minimization, enhances training stability and sample efficiency compared to existing RL-based methods. Empirical results demonstrate the effectiveness and superior reward optimization of our approach across diverse tasks in protein, small molecule, and regulatory DNA design.

Applications · Chemistry and Drug Discovery

Aditya Sengar, Jiying Zhang, Pierre Vandergheynst, PATRICK BARTH

Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult to identify, restricting their ability to model complex switching mechanisms between metastable states. A recent generative model, LD-FPG, demonstrated that this problem could be bypassed by learning to sample the static equilibrium ensemble as all-atom deformations from a reference structure, establishing a powerful method for all-atom ensemble generation. However, while this approach successfully captures a system's probable conformations, it does not model the temporal evolution between them. We introduce the Graph Latent Dynamics Propagator (GLDP), a modular component for simulating dynamics within the learned latent space of LD-FPG. We then compare three classes of propagators: (i) score-guided Langevin dynamics, (ii) Koopman-based linear operators, and (iii) autoregressive neural networks. Within a unified encoder–propagator–decoder framework, we evaluate long-horizon stability, backbone and side-chain ensemble fidelity, and temporal kinetics via TICA. Benchmarks on systems ranging from small peptides to mixed-topology proteins and large GPCRs reveal that autoregressive neural networks deliver the most robust long rollouts and coherent physical timescales; score-guided Langevin best recovers side-chain thermodynamics when the score is well learned; and Koopman provides an interpretable, lightweight baseline that tends to damp fluctuations. These results clarify the trade-offs among propagators and offer practical guidance for latent-space simulators of all-atom protein dynamics.