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Applications · Chemistry and Drug Discovery

Haichuan Tan, Bowen Gao, Jiaxin Li, Yinjun Jia, Wenyu Zhu, Wenxuan Xie, Yihong Liu, Yanwen Huang, Jianhui Wang, Yuanhuan Mo 等

A significant portion of disease-relevant proteins remain undruggable due to shallow, flexible, or otherwise ill-defined binding pockets that hinder conventional molecule screening. Fragment-based drug discovery (FBDD) offers a promising alternative, as small, low-complexity fragments can flexibly engage shallow, transient, or cryptic binding pockets that are often inaccessible to conventional drug-like molecules. However, fragment screening remains difficult due to weak binding signals, limited experimental throughput, and a lack of computational tools tailored for this setting. In this work, we introduce FragBench, the first benchmark for fragment-level virtual screening on undruggable targets. We construct a high-quality dataset through multi-agent LLM–human collaboration and interaction-based fragment labeling. To address the core modeling challenge, we propose a novel tri-modal contrastive learning framework FragCLIP that jointly encodes fragments, full molecules, and protein pockets. Our method significantly outperforms baselines like docking software and other ML based methods. Moreover, we demonstrate that retrieved fragments can be effectively expanded or linked into larger compounds with improved predicted binding affinity, supporting their utility as viable starting points for drug design.

Applications · Chemistry and Drug Discovery

Haokai Hong, Wanyu LIN, Chusong Zhang, KC Tan

Geometric graph neural networks (Geo-GNNs) have revolutionized molecular dynamics (MD) simulations by providing accurate and fast energy and force predictions. However, minor prediction errors could still destabilize MD trajectories in real MD simulations due to the limited coverage of molecular conformations in training datasets. Existing methods that focus on in-distribution predictions often fail to address extrapolation to unseen conformations, undermining the simulation stability. To tackle this, we propose Geometric Graph Neural Diffusion (GGND), a novel framework that can capture geometrically invariant topological features, thereby alleviating error accumulation and ensuring stable MD simulations. The core of our framework is that it iteratively refines atomic representations, enabling instantaneous information flow between arbitrary atomic pairs while maintaining equivariance. Our proposed GGND is a plug-and-play module that can seamlessly integrate with existing local equivariant message-passing frameworks, enhancing their predictive performance and simulation stability. We conducted sets of experiments on the 3BPA and SAMD23 benchmark datasets, which encompass diverse molecular conformations across varied temperatures. We also ran real MD simulations to evaluate the stability. GGND outperforms baseline models in both accuracy and stability under significant topological shifts, advancing stable molecular modeling for real-world applications.

Applications · Chemistry and Drug Discovery

Kacper Kapusniak, Cristian Gabellini, Michael Bronstein, Prudencio Tossou, Francesco Di Giovanni

Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this, several generative models have been proposed to generate surrogate trajectories at lower cost. Yet, these models typically learn a fixed-lag transition density, causing the training signal to be dominated by frequent but uninformative transitions. We introduce a new class of generative models, **MSM Emulators**, which instead learn to sample transitions across discrete states defined by an underlying Markov State Model (MSM). We instantiate this class with Markov Space Flow Matching (MarS-FM), whose sampling offers more than two orders of magnitude speedup compared to implicit- or explicit-solvent MD simulations. We benchmark Mars-FM ability to reproduce MD statistics through structural observables such as RMSD, radius of gyration, and secondary structure content. Our evaluation spans protein domains (up to 500 residues) with significant chemical and structural diversity, including unfolding events, and enforces strict sequence dissimilarity between training and test sets to assess generalization. Across all metrics, MarS-FM outperforms existing methods, often by a substantial margin.

Applications · Chemistry and Drug Discovery

Junqi Liu, Xiaoyang Hou, Chence Shi, Xin Liu, Zhi Yang, Jian Tang

Protein sequence design must balance designability, defined as the ability to recover a target backbone, with multiple, often competing, developability properties such as solubility, thermostability, and expression. Existing approaches address these properties through post hoc mutation, inference-time biasing, or retraining on property-specific subsets, yet they are target dependent and demand substantial domain expertise or careful hyperparameter tuning. In this paper, we introduce ProtAlign, a multi-objective preference alignment framework that fine-tunes pretrained inverse folding models to satisfy diverse developability objectives while preserving structural fidelity. ProtAlign employs a semi-online Direct Preference Optimization strategy with a flexible preference margin to mitigate conflicts among competing objectives and constructs preference pairs using in silico property predictors. Applied to the widely used ProteinMPNN backbone, the resulting model MoMPNN enhances developability without compromising designability across tasks including sequence design for CATH 4.3 crystal structures, de novo generated backbones, and real-world binder design scenarios, making it an appealing framework for practical protein sequence design.

Applications · Chemistry and Drug Discovery

Xuan Zhang, Haiyang Yu, Chengdong Wang, Jacob Helwig, Shuiwang Ji, Xiaofeng Qian

We aim to learn wavefunctions simulated by time-dependent density functional theory (TDDFT), which can be efficiently represented as linear combination coefficients of atomic orbitals. In real-time TDDFT, the electronic wavefunctions of a molecule evolve over time in response to an external excitation, enabling first-principles predictions of physical properties such as optical absorption, electron dynamics, and high-order response. However, conventional real-time TDDFT relies on time-consuming propagation of all occupied states with fine time steps. In this work, we propose OrbEvo, which is based on an equivariant graph transformer architecture and learns to evolve the full electronic wavefunction coefficients across time steps. First, to account for external field, we design an equivariant conditioning to encode both strength and direction of external electric field and break the symmetry from SO(3) to SO(2). Furthermore, we design two OrbEvo models, OrbEvo-WF and OrbEvo-DM, using wavefunction pooling and density matrix as interaction method, respectively. Motivated by the central role of the density functional in TDDFT, OrbEvo-DM encodes the density matrix aggregated from all occupied electronic states into feature vectors via tensor contraction, providing a more intuitive approach to learn the time evolution operator. We adopt a training strategy specifically tailored to limit the error accumulation of time-dependent wavefunctions over autoregressive rollout. To evaluate our approach, we generate TDDFT datasets consisting of 5,000 different molecules in the QM9 dataset and 1,500 molecular configurations of the malonaldehyde molecule in the MD17 dataset. Results show that our OrbEvo model accurately captures quantum dynamics of excited states under external field, including time-dependent wavefunctions, time-dependent dipole moment, and optical absorption spectra characterized by dipole oscillator strength. It also shows strong generalization capability on the diverse molecules in the QM9 dataset. Our dataset is available at https://huggingface.co/divelab, and our code is available as part of the AIRS library https://github.com/divelab/AIRS/.

Applications · Chemistry and Drug Discovery

Yikai Liu, Haoyang Zheng, Lining Mao, Yanbin Wang, Ming Chen, Guang Lin

Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes, but its application is limited by high computational cost. We present ProTDyn, a foundation protein language model that unifies conformational ensemble generation and multi-timescale dynamics modeling within a single framework. Unlike prior approaches that treat these tasks separately, ProTDyn allows flexible i.i.d ensemble sampling and dynamic trajectory simulation. Across diverse protein systems, ProTDyn yields thermodynamically consistent ensembles, faithfully reproduces dynamical properties over multiple timescales, and generalizes to proteins beyond its training data—offering a scalable and efficient alternative to conventional MD simulations.

Applications · Chemistry and Drug Discovery

Mihir Bafna, Bowen Jing, Bonnie Berger

Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico gold standard, its high computational cost limits scalability. We present DynaProt, a lightweight, SE(3)-invariant framework that predicts rich descriptors of protein dynamics directly from static structures. By casting the problem through the lens of multivariate Gaussians, DynaProt estimates dynamics at two complementary scales: (1) per-residue marginal anisotropy as covariance matrices capturing local flexibility, and (2) joint scalar covariances encoding pairwise dynamic coupling across residues. From these dynamics outputs, DynaProt achieves high accuracy in predicting residue-level flexibility (RMSF) and, remarkably, enables reasonable reconstruction of the full covariance matrix for fast ensemble generation. Notably, it does so using orders of magnitude fewer parameters than prior methods. Our results highlight the potential of direct protein dynamics prediction as a scalable alternative to existing methods.

Applications · Chemistry and Drug Discovery

Seonghyun Park, Kiyoung Seong, Soojung Yang, Rafael Gomez-Bombarelli, Sungsoo Ahn

Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation along key reaction pathways, which are defined by collective variables (CVs). However, identifying effective CVs that capture the slow, macroscopic dynamics of a system remains a major bottleneck. This work proposes a novel framework coined BioEmu-CV that learns these essential CVs automatically from BioEmu, a recently proposed foundation model for generating protein equilibrium samples. In particular, we re-purpose BioEmu to learn time-lagged generation conditioned on the learned CV, i.e., predict the distribution of molecular states after a certain amount of time. This training process promotes the CV to encode only the slow, long-term information while disregarding fast, random fluctuations. We validate our learned CV on fast-folding proteins with two key applications: (1) estimating free energy differences using on-the-fly probability enhanced sampling and (2) sampling transition paths with steered molecular dynamics. Our empirical study also serves as a new systematic and comprehensive benchmark for MLCVs on fast-folding proteins larger than Alanine Dipeptide.

Applications · Chemistry and Drug Discovery

Hyunjin Seo, Taewon Kim, Sihyun Yu, Sungsoo Ahn

Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that naively applying standards MDMs to molecules leads to severe performance degradation. We trace this critical issue to a *state-clashing problem*-where the forward diffusion trajectories of distinct molecules collapse into a common state, resulting in a mixture of reconstruction targets that cannot be learned with a typical reverse diffusion with unimodal predictions. To mitigate this, we propose **M**asked **E**lement-wise **L**earnable **D**iffusion (**MELD**) that orchestrates per-element corruption trajectories to avoid collisions between different molecular graphs. This is realized through a parameterized noise scheduling network that learns distinct corruption rates for individual graph elements, *i.e.*, atoms and bonds. Across extensive experiments, **MELD** achieves 100\% chemical validity in unconditional generation on QM9 and ZINC250K datasets, while markedly improving distributional and property alignment over standard MDMs on both conditional and unconditioned generation.

Applications · Chemistry and Drug Discovery

Jinjia Feng, Zhewei Wei, Taifeng Wang, Zongyang Qiu

Molecular representations that fully capture geometric parameters such as bond angles and torsion angles are crucial for accurately predicting important molecular properties including enzyme catalytic activity, drug bioactivity, and molecular spectral characteristics, as demonstrated by extensive studies. However, current molecular graph representation learning approaches represent molecular geometric parameters only indirectly through combinations of atoms and bonds, neglecting the spatial relationships and interactions between these higher-order geometric structures. In this paper, we propose \textbf{TetraGT} (\textbf{Tetra}hedral \textbf{G}eometry-Driven Explicit \textbf{T}oken Interactions with Graph Transformer), a novel architecture that directly models molecular geometric parameters. Based on the spatial solid geometry theory of face angle and dihedral angle inequality, TetraGT explicitly represents bond angles and torsion angles as structured tokens for the first time, directly reflecting their intrinsic role in determining the molecular conformational stability and properties. Through our designed spatial tetrahedral attention mechanism, TetraGT achieves highly selective direct communication between structural tokens. Experimental results demonstrate that TetraGT achieves superior performance on the PCQM4Mv2 and OC20 IS2RE benchmarks. We also apply our pre-trained TetraGT model to downstream tasks including QM9, PDBBind, Peptides and LIT-PCBA, demonstrating that TetraGT delivers excellent results in transfer learning scenarios and shows scalability with increasing molecular size.

Applications · Chemistry and Drug Discovery

Emily Jin, Andrei Nica, Mikhail Galkin, Jarrid Rector-Brooks, Kin Long Kelvin Lee, Santiago Miret, Frances Arnold, Michael Bronstein, Joey Bose, Alexander Tong 等

Accurately predicting experimentally realizable 3D molecular crystal structures from their 2D chemical graphs is a long-standing open challenge in computational chemistry called crystal structure prediction (CSP). Efficiently solving this problem has implications ranging from pharmaceuticals to organic semiconductors, as crystal packing directly governs the physical and chemical properties of organic solids. In this paper, we introduce OXtal, a large-scale 100M parameter all-atom diffusion model that directly learns the conditional joint distribution over intramolecular conformations and periodic packing. To efficiently scale OXtal, we abandon explicit equivariant architectures imposing inductive bias arising from crystal symmetries in favor of data augmentation strategies. We further propose a novel crystallization-inspired lattice-free training scheme, Stoichiometric Stochastic Shell Sampling ($S^4$), that efficiently captures long-range interactions while sidestepping explicit lattice parametrization---thus enabling more scalable architectural choices at all-atom resolution. By leveraging a large dataset of 600K experimentally validated crystal structures (including rigid and flexible molecules, co-crystals, and solvates), OXtal achieves orders-of-magnitude improvements over prior ab initio machine learning CSP methods, while remaining orders of magnitude cheaper than traditional quantum-chemical approaches. Specifically, OXtal recovers experimental structures with conformer $\mathrm{RMSD}_1<0.5$ Å and attains over 80% packing similarity rate, demonstrating its ability to model both thermodynamic and kinetic regularities of molecular crystallization.

Applications · Chemistry and Drug Discovery

Xinzhe Yuan, Zhuo Chen, Jianshu Zhang, Huan Xiong, Nanyang Ye, Yuqiang Li, Qinying Gu

Scientific discovery is increasingly constrained by costly experiments and limited budgets, making efficient optimization essential for AI for science. Bayesian Optimization (BO), while widely adopted for balancing exploration and exploitation, suffers from slow cold-start performance and poor scalability in high-dimensional settings, limiting its effectiveness in real-world scientific applications. To address these challenges, we propose LLM-Guided Bayesian Optimization (LGBO), the first LLM preference-guided BO framework that continuously integrates the semantic reasoning of large language models (LLMs) into the optimization loop. Unlike prior works that use LLMs only for warm-start initialization or candidate generation, LGBO introduces a region-lifted preference mechanism that embeds LLM-driven preferences into every iteration, shifting the surrogate mean in a stable and controllable way. Theoretically, we prove that LGBO is not perform significantly worse than standard BO in the worst case, while achieving significantly faster convergence when preferences align with the objective. Empirically, LGBO achieves consistent improvements across diverse dry benchmarks in physics, chemistry, biology, and materials science. Most notably, in a new wet-lab optimization of Fe–Cr battery electrolytes, LGBO reaches \textbf{90\% of the best observed value within 6 iterations}, whereas standard BO and existing LLM-augmented baselines require more than 10 iterations. Together, the results suggest that LGBO offers a promising direction for integrating LLMs into scientific optimization workflows.

Applications · Chemistry and Drug Discovery

Riccardo De Santi, Kimon Protopapas, Ya-Ping Hsieh, Andreas Krause

Flow and diffusion models are typically pre-trained on limited available data (e.g., molecular samples), covering only a fraction of the valid design space (e.g., the full molecular space). As a consequence, they tend to generate samples from only a narrow portion of the feasible domain. This is a fundamental limitation for scientific discovery applications, where one typically aims to sample valid designs beyond the available data distribution. To this end, we address the challenge of leveraging access to a verifier (e.g., an atomic bonds checker), to adapt a pre-trained flow model so that its induced density expands beyond regions of high data availability, while preserving samples validity. We introduce formal notions of strong and weak verifiers and propose algorithmic frameworks for global and local flow expansion via probability-space optimization. Then, we present Flow Expander (FE), a scalable mirror descent scheme that provably tackles both problems by verifier-constrained entropy maximization over the flow process noised state space. Next, we provide a thorough theoretical analysis of the proposed method, and state convergence guarantees under both idealized and general assumptions. Ultimately, we empirically evaluate our method on both illustrative, yet visually interpretable settings, and on a molecular design task showcasing the ability of FE to expand a pre-trained flow model increasing conformer diversity while preserving validity.

Applications · Chemistry and Drug Discovery

Jungseob Yi, Seoyoung Choi, Sun Kim, Sangseon Lee

Virtual screening (VS) aims to identify bioactive compounds from vast chemical libraries, but remains difficult in low-label regimes where only a few actives are known. Existing methods largely rely on general-purpose molecular fingerprints and overlook class-discriminative substructures critical to bioactivity. Moreover, they consider molecules independently, limiting effectiveness in low-label regimes. We introduce SubDyve, a network-based VS framework that constructs a subgraph-aware similarity network and propagates activity signals from a small known actives. When few active compounds are available, SubDyve performs iterative seed refinement, incrementally promoting new candidates based on local false discovery rate. This strategy expands the seed set with promising candidates while controlling false positives from topological bias and overexpansion. We evaluate SubDyve on ten DUD-E targets under zero-shot conditions and on the CDK7 target with a 10-million-compound ZINC dataset. SubDyve consistently outperforms existing fingerprint or embedding-based approaches, achieving margins of up to +34.0 on the BEDROC and +24.6 on the $EF_{1\\%}$ metric.

Applications · Chemistry and Drug Discovery

Botian Wang, Yawen Ouyang, Yaohui Li, Mianzhi Pan, yuanhang tang, Haorui Cui, Yiqun Wang, Jianbing Zhang, Xiaonan Wang, Wei-Ying Ma 等

Deep learning methods for material property prediction have been widely explored to advance materials discovery. However, the prevailing pre-train paradigm often fails to address the inherent diversity and disparity of material tasks. To overcome these challenges, we introduce MoMa, a simple Modular framework for Materials that first trains specialized modules across a wide range of tasks and then adaptively composes synergistic modules tailored to each downstream scenario. Evaluation across 17 datasets demonstrates the superiority of MoMa, with a substantial 14% average improvement over the strongest baseline. Few-shot and module scaling experiments further highlight MoMa's potential for real-world applications. Pioneering a new paradigm of modular material learning, MoMa will be open-sourced to foster broader community collaboration.

Applications · Chemistry and Drug Discovery

Sazan Mahbub, Souvik Kundu, Eric P Xing

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local structural constraints. Existing deep learning approaches achieve strong recovery rates, however, lack explicit mechanisms to reuse fine-grained structure-sequence patterns conserved across natural proteins. To mitigate this, we present PRISM a multimodal retrieval-augmented generation framework for inverse folding. PRISM retrieves fine-grained representations of potential motifs from known proteins and integrates them with a hybrid self-cross attention decoder. PRISM is formulated as a latent-variable probabilistic model and implemented with an efficient approximation, combining theoretical grounding with practical scalability. Experiments across multiple benchmarks, including CATH-4.2, TS50, TS500, CAMEO 2022, and the PDB date split, demonstrate the fine-grained multimodal retrieval efficacy of PRISM in yielding SoTA perplexity and amino acid recovery, while also improving the foldability metrics (RMSD, TM-score, pLDDT).

Applications · Chemistry and Drug Discovery

Hannah Lawrence, Elyssa Hofgard, Vasco Portilheiro, Yuxuan Chen, Tess Smidt, Robin Walters

Symmetry-aware methods for machine learning, such as data augmentation and equivariant architectures, encourage correct model behavior on all transformations (e.g. rotations or permutations) of the original dataset. These methods can improve generalization and sample efficiency, under the assumption that the transformed datapoints are highly probable, or "important", under the test distribution. In this work, we develop a method for critically evaluating this assumption. In particular, we propose a metric to quantify the amount of symmetry breaking in a dataset, via a two-sample classifier test that distinguishes between the original dataset and its randomly augmented equivalent. We validate our metric on synthetic datasets, and then use it to uncover surprisingly high degrees of symmetry-breaking in several benchmark point cloud datasets, constituting a severe form of dataset bias. We show theoretically that distributional symmetry-breaking can prevent invariant methods from performing optimally even when the underlying labels are truly invariant, for invariant ridge regression in the infinite feature limit. Empirically, the implication for symmetry-aware methods is dataset-dependent: equivariant methods still impart benefits on some symmetry-biased datasets, but not others, particularly when the symmetry bias is predictive of the labels. Overall, these findings suggest that understanding equivariance — both when it works, and why — may require rethinking symmetry biases in the data.

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

Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For \textit{de novo} generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproducible.

Applications · Chemistry and Drug Discovery

Pablo Lemos, Zane Beckwith, Sasaank Bandi, Maarten Van Damme, Jordan Crivelli-Decker, Benjamin Shields, Thomas Merth, Punit Jha, Nicola De Mitri, Tiffany Callahan 等

Accurate prediction of protein-ligand binding affinities remains a cornerstone problem in drug discovery. While binding affinity is inherently dictated by the 3D structure and dynamics of protein-ligand complexes, current deep learning approaches are limited by the lack of high-quality experimental structures with annotated binding affinities. To address this limitation, we introduce the Structurally Augmented IC50 Repository (SAIR), the largest publicly available dataset of protein-ligand 3D structures with associated activity data. The dataset comprises $5,244,285$ structures across $1,048,857$ unique protein-ligand systems, curated from the ChEMBL and BindingDB databases, which were then computationally folded using the Boltz-1x model. We provide a comprehensive characterization of the dataset, including distributional statistics of proteins and ligands, and evaluate the structural fidelity of the folded complexes using PoseBusters. Our analysis reveals that approximately $3 \%$ of structures exhibit physical anomalies, predominantly related to internal energy violations. As an initial demonstration, we benchmark several binding affinity prediction methods, including empirical scoring functions (Vina, Vinardo), a 3D convolutional neural network (Onionnet-2), and a graph neural network (AEV-PLIG). While machine learning-based models consistently outperform traditional scoring function methods, neither exhibit a high correlation with ground truth affinities, highlighting the need for models specifically fine-tuned to synthetic structure distributions. This work provides a foundation for developing and evaluating next-generation structure and binding-affinity prediction models and offers insights into the structural and physical underpinnings of protein-ligand interactions. The link to the data will be added upon publication, to preserve anonymity of the submission.