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Applications · Chemistry and Drug Discovery

Seongsu Kim, Nayoung Kim, Dongwoo Kim, Sungsoo Ahn

Density functional theory (DFT) is a fundamental method for simulating quantum chemical properties, but it remains expensive due to the iterative self-consistent field (SCF) process required to solve the Kohn–Sham equations. Recently, deep learning methods are gaining attention as a way to bypass this step by directly predicting the Hamiltonian. However, they rely on deterministic regression and do not consider the highly structured nature of Hamiltonians. In this work, we propose QHFlow, a high-order equivariant flow matching framework that generates Hamiltonian matrices conditioned on molecular geometry. Flow matching models continuous-time trajectories between simple priors and complex targets, learning the structured distributions over Hamiltonians instead of direct regression. To further incorporate symmetry, we use a neural architecture that predicts SE(3)-equivariant vector fields, improving accuracy and generalization across diverse geometries. To further enhance physical fidelity, we additionally introduce a fine-tuning scheme to align predicted orbital energies with the target. QHFlow achieves state-of-the-art performance, reducing Hamiltonian error by 71% on MD17 and 53% on QH9. Moreover, we further show that QHFlow accelerates the DFT process without trading off the solution quality when initializing SCF iterations with the predicted Hamiltonian, significantly reducing the number of iterations and runtime.

Applications · Chemistry and Drug Discovery

Andrew Liu, Axel Elaldi, Nicholas Franklin, Nathan Russell, Gurinder Atwal, Yih-En Ban, Olivia Viessmann

Invariant Point Attention (IPA) is a key algorithm for geometry-aware modeling in structural biology, central to many protein and RNA models. However, its quadratic complexity limits the input sequence length. We introduce FlashIPA, a factorized reformulation of IPA that leverages hardware-efficient FlashAttention to achieve linear scaling in GPU memory and wall-clock time with sequence length. FlashIPA matches or exceeds standard IPA performance while substantially reducing computational costs. FlashIPA extends training to previously unattainable lengths, and we demonstrate this by re-training generative models without length restrictions and generating structures of thousands of residues. FlashIPA is available at https://github.com/flagshippioneering/flash_ipa.

Applications · Chemistry and Drug Discovery

Zhiqiang Zhong, Davide Mottin

Recent studies in *Machine Learning* (ML) for biological research focus on investigating molecular properties to accelerate drug discovery. However, limited labeled molecular data often hampers the performance of ML models. A common strategy to mitigate data scarcity is leveraging auxiliary learning tasks to provide additional supervision, but selecting effective auxiliary tasks requires substantial domain expertise and manual effort, and their inclusion does not always guarantee performance gains. To overcome these challenges, we introduce *Automatic Auxiliary Task Selection* (AutAuT), a fully automated framework that seamlessly retrieves auxiliary tasks using large language models and adaptively integrates them through a novel *gradient alignment* weighting mechanism. By automatically emphasizing auxiliary tasks aligned with the primary objective, AutAuT significantly enhances predictive accuracy while reducing negative impacts from irrelevant tasks. Extensive evaluations demonstrate that AutAuT outperforms *10* auxiliary task-based approaches and *18* advanced molecular property prediction models.

Applications · Chemistry and Drug Discovery

HUANLEI GUO, Song LIU, Bingyi Jing

Molecular docking is a fundamental technique in structure-based drug discovery, playing a critical role in predicting the binding poses of protein-ligand complexes. While traditional docking methods are generally reliable, they are often computationally expensive. Recent deep learning (DL) approaches have substantially accelerated docking and improved prediction accuracy; however, they frequently generate conformations that lack physical plausibility due to insufficient integration of physical priors. To deal with these challenges, we propose ForceFM, a novel force-guided model that integrates a force-guided network into the generation process, steering ligand poses toward low-energy, physically realistic conformations. Force guidance also halves inference cost compared with the unguided approaches. Importantly, replacing the guiding potential with diverse energy functions-including Vina, Glide, Gnina, and Confscore-preserves or improves performance, underscoring the method's generality and robustness. These results highlight ForceFM's ability to set new standards in docking accuracy and physical consistency, surpassing the limitations of previous methods. Code is available at \url{https://github.com/Guhuary/ForceFM}.

Applications · Chemistry and Drug Discovery

Robin Yadav, Qi Yan, Guy Wolf, Joey Bose, Renjie Liao

A fundamental challenge in organic chemistry is identifying and predicting the sequence of reactions that synthesize a desired target molecule. Due to the combinatorial nature of the chemical search space, single-step reactant prediction—i.e., single-step retrosynthesis—remains difficult, even for state-of-the-art template-free generative methods. These models often struggle to produce an accurate yet diverse set of feasible reactions in a chemically rational manner. In this paper, we propose RETRO SYNFLOW (RSF), a discrete flow-matching framework that formulates single-step retrosynthesis as a Markov bridge between a given product molecule and its corresponding reactants. Unlike prior approaches, RSF introduces a reaction center identification step to extract intermediate structures, or synthons, which serve as a more informative and structured source distribution for the discrete flow model. To further improve the diversity and chemical feasibility of generated samples, RSF incorporates Feynman-Kac (FK) steering with Sequential Monte Carlo (SMC) resampling at inference time. This approach leverages a learned forward-synthesis reward oracle to guide the generation process toward more promising reactant candidates. Empirically, RSF substantially outperforms the previous state-of-the-art methods in top-1 accuracy. In addition, FK-steering significantly improves round-trip accuracy, demonstrating stronger chemical validity and synthetic feasibility, all while maintaining competitive top-k performance. These results establish RSF as a new leading approach for single-step retrosynthesis prediction.

Applications · Chemistry and Drug Discovery

Mianchu Wang, Giovanni Montana

Retrosynthesis planning aims to decompose target molecules into available building blocks, forming a synthetic tree where each internal node represents an intermediate compound and each leaf ideally corresponds to a purchasable reactant. However, this tree becomes invalid if any leaf node is not a valid building block, making the planning process vulnerable to the "weakest link" in the synthetic route. Existing methods often optimise for average performance across branches, failing to account for this worst-case sensitivity. In this paper, we reframe retrosynthesis as a worst-path optimisation problem within tree-structured Markov Decision Processes (MDPs). We prove that this formulation admits a unique optimal solution and provides monotonic improvement guarantees. Building on this insight, we introduce Interactive Retrosynthesis Planning (InterRetro), a method that interacts with the tree MDP, learns a value function for worst-path outcomes, and improves its policy through self-imitation, preferentially reinforcing past decisions with high estimated advantage. Empirically, InterRetro achieves state-of-the-art results — solving 100\% of targets on the Retro*-190 benchmark, shortening synthetic routes by 4.9\%, and achieving promising performance using only 10\% of the training data.

Applications · Chemistry and Drug Discovery

Giannis Daras, Jeffrey Ouyang-Zhang, Krithika Ravishankar, Constantinos Daskalakis, Adam Klivans, Daniel Diaz

We present Ambient Protein Diffusion, a framework for training protein diffusion models that generates structures with unprecedented diversity and quality. State-of-the-art generative models are trained on computationally derived structures from AlphaFold2 (AF), as experimentally determined structures are relatively scarce. The resulting models are therefore limited by the quality of synthetic datasets. Since the accuracy of AF predictions degrades with increasing protein length and complexity, de novo generation of long, complex proteins remains challenging. Ambient Protein Diffusion overcomes this problem by treating low-confidence AF structures as corrupted data. Rather than simply filtering out low-quality AF structures, our method adjusts the diffusion objective for each structure based on its corruption level, allowing the model to learn from both high and low quality structures. Empirically, ambient protein diffusion yields major improvements: on proteins with 700 residues, diversity increases from 45% to 85% from the previous state-of-the-art, and designability improves from 70% to 88%.

Applications · Chemistry and Drug Discovery

Sihan Wang, Wenjie Du, Qing Zhu, Yang Wang

Artificial intelligence (AI) has played a transformative role in chemical research, greatly facilitating the prediction of small molecule properties, simulation of catalytic processes, and material design. These advances are driven by increases in computing power, open source machine learning frameworks, and extensive chemical datasets. However, a persistent challenge is the limited amount of high-quality real-world data, while models calculated based on large amounts of theoretical data are often costly and difficult to deploy, which hinders the applicability of AI models in real-world scenarios. In this study, we enhance the prediction of solute-solvent properties by proposing a novel sample selection method: the iterative core subset extraction (CSIE) framework. CSIE iteratively updates the core sample subset based on information gain to remove redundant features in theoretical data and optimize the performance of the model on real chemical datasets. Furthermore, we introduce an asymmetric molecular interaction graph neural network (AMGNN) that combines positional information and bidirectional edge connections to simulate real-world chemical reaction scenarios to better capture solute-solvent interactions. Experimental results show that our method can accurately extract the core subset and improve the prediction accuracy.

Applications · Chemistry and Drug Discovery

Rishwanth Raghu, Axel Levy, Gordon Wetzstein, Ellen Zhong

Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring heuristic MSA subsampling approaches for generating alternative states. In parallel, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for imaging near-native structural heterogeneity, but is challenged by arduous pipelines to transform raw experimental data into atomic models. Here, we bridge the gap between these modalities, combining cryo-EM density maps with the rich sequence and biophysical priors learned by protein structure prediction models. Our method, CryoBoltz, guides the sampling trajectory of a pretrained biomolecular structure prediction model using both global and local structural constraints derived from density maps, driving predictions towards conformational states consistent with the experimental data. We demonstrate that this flexible yet powerful inference-time approach allows us to build atomic models into heterogeneous cryo-EM maps across a variety of dynamic biomolecular systems including transporters and antibodies.

Applications · Chemistry and Drug Discovery

Brandon Wood, Misko Dzamba, Xiang Fu, Meng Gao, Muhammed Shuaibi, Luis Barroso-Luque, Kareem Abdelmaqsoud, Vahe Gharakhanyan, John Kitchin, Daniel Levine 等

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, we present a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only $\sim$50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to build increasingly capable AI models.

Applications · Chemistry and Drug Discovery

Guanlue Li, Xufeng Zhao, Fang Wu, Sören Laue

Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

Applications · Chemistry and Drug Discovery

Chang Wu, ZHIYUAN LIU, Wen Shu, Liang Wang, Yanchen Luo, Wenqiang Lei, Yatao Bian, Junfeng Fang, Xiang Wang

Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL). However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D structure leakage to the decoder, while still providing sufficient 2D context for reconstructing re-masked atoms. To address these challenges, we propose 3D-GSRD: a 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding. The core innovation of 3D-GSRD lies in its Selective Re-mask Decoding (SRD), which re-masks only 3D-relevant information from encoder representations while preserving the 2D graph structures. This SRD is synergistically integrated with a 3D Relational-Transformer (3D-ReTrans) encoder alongside a structure-independent decoder. We analyze that SRD, combined with the structure-independent decoder, enhances the encoder's role in MRL. Extensive experiments show that 3D-GSRD achieves strong downstream performance, setting a new state-of-the-art on 7 out of 8 targets in the widely used MD17 molecular property prediction benchmark. The code is released at https://github.com/WuChang0124/3D-GSRD.

Applications · Chemistry and Drug Discovery

Pedro O. Pinheiro, Pan Kessel, Aya Ismail, Sai Pooja Mahajan, Kyunghyun Cho, Saeed Saremi, Nataša Tagasovska

Generative modeling is increasingly important for data-driven computational design. Conventional approaches pair a generative model with a discriminative model to select or guide samples toward optimized designs. Yet discriminative models often struggle in data-scarce settings, common in scientific applications, and are unreliable in the tails of the distribution where optimal designs typically lie. We introduce generative property enhancer (GPE), an approach that implicitly guides generation by matching samples with lower property values to higher-value ones. Formulated as conditional density estimation, our framework defines a target distribution with improved properties, compelling the generative model to produce enhanced, diverse designs without auxiliary predictors. GPE is simple, scalable, end-to-end, modality-agnostic, and integrates seamlessly with diverse generative model architectures and losses. We demonstrate competitive empirical results on standard _in silico_ offline (non-sequential) protein fitness optimization benchmarks. Finally, we propose iterative training on a combination of limited real data and self-generated synthetic data, enabling extrapolation beyond the original property ranges.

Applications · Chemistry and Drug Discovery

Johann Flemming Gloy, Simon Olsson

Flow and diffusion-based models have emerged as powerful tools for scientific applications, particularly for sampling non-normalized probability distributions, as exemplified by Boltzmann Generators (BGs). A critical challenge in deploying these models is their reliance on sample likelihood computations, which scale prohibitively with system size $n$, often rendering them infeasible for large-scale problems. To address this, we introduce $\textit{HollowFlow}$, a flow-based generative model leveraging a novel non-backtracking graph neural network (NoBGNN). By enforcing a block-diagonal Jacobian structure, HollowFlow likelihoods are evaluated with a constant number of backward passes in $n$, yielding speed-ups of up to $\mathcal{O}(n^2)$: a significant step towards scaling BGs to larger systems. Crucially, our framework generalizes: $\textbf{any equivariant GNN or attention-based architecture}$ can be adapted into a NoBGNN. We validate HollowFlow by training BGs on two different systems of increasing size. For both systems, the sampling and likelihood evaluation time decreases dramatically, following our theoretical scaling laws. For the larger system we obtain a $10^2\times$ speed-up, clearly illustrating the potential of HollowFlow-based approaches for high-dimensional scientific problems previously hindered by computational bottlenecks.

Applications · Chemistry and Drug Discovery

Charlie Tan, Majdi Hassan, Leon Klein, Saifuddin Syed, Dominique Beaini, Michael Bronstein, Alexander Tong, Kirill Neklyudov

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in-full for each system of interest. The widespread success of generative models has inspired interest into overcoming this limitation through learning sampling algorithms. Despite performing on par with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We prove that deep learning enables the design of scalable and transferable samplers by introducing Ensemble, a 200 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Ensemble draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Ensemble as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve superior performance to established methods such as sequential Monte Carlo. We open-source the Ensemble codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.

Applications · Chemistry and Drug Discovery

Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily Makowski, Andrew Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

Applications · Chemistry and Drug Discovery

Jason Yang, Wenda Chu, Daniel Khalil, Raul Astudillo, Bruce Wittmann, Frances Arnold, Yisong Yue

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.

Applications · Chemistry and Drug Discovery

Li Hao, He CAO, Bin Feng, Daniel Shao, Robert Tang, Zhiyuan Yan, Yonghong Tian, Li Yuan, Yu Li

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. We further provide ChemCoTDataset, a pioneering 22,000-instance chemical reasoning dataset with expert-annotated chains of thought to facilitate LLM fine-tuning. By providing annotated trainable datasets, a reasoning taxonomy, and baseline evaluations, our work bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Applications · Chemistry and Drug Discovery

Subhojyoti Khastagir, KISHALAY DAS, Pawan Goyal, Seung-Cheol Lee, Satadeep Bhattacharjee, niloy ganguly

Recent advances in generative modeling have shown significant promise in designing novel periodic crystal structures. Existing approaches typically rely on either large language models (LLMs) or equivariant denoising models, each with complementary strengths: LLMs excel at handling discrete atomic types but often struggle with continuous features such as atomic positions and lattice parameters, while denoising models are effective at modeling continuous variables but encounter difficulties in generating accurate atomic compositions. To bridge this gap, we propose CrysLLMGen, a hybrid framework that integrates an LLM with a diffusion model to leverage their complementary strengths for crystal material generation. During sampling, CrysLLMGen first employs a fine-tuned LLM to produce an intermediate representation of atom types, atomic coordinates, and lattice structure. While retaining the predicted atom types, it passes the atomic coordinates and lattice structure to a pre-trained equivariant diffusion model for refinement. Our framework outperforms state-of-the-art generative models across several benchmark tasks and datasets. Specifically, CrysLLMGen not only achieves a balanced performance in terms of structural and compositional validity but also generates more stable and novel materials compared to LLM-based and denoising-based models Furthermore, CrysLLMGen exhibits strong conditional generation capabilities, effectively producing materials that satisfy user-defined constraints. Code is available at \url{https://github.com/kdmsit/crysllmgen}

Applications · Chemistry and Drug Discovery

Dahao Xu, Jiahua Rao, Mingming Zhu, Jixian Zhang, Wei Lu, Shuangjia Zheng, Yuedong Yang

Predicting changes in binding free energy ($\Delta\Delta G$) is essential for understanding protein-protein interactions, which are critical in drug design and protein engineering. However, existing methods often rely on pre-trained knowledge and heuristic features, limiting their ability to accurately model complex mutation effects, particularly higher-order and many-body interactions. To address these challenges, we propose H3-DDG, a Hypergraph-driven Hierarchical network to capture Higher-order many-body interactions across multiple scales. By introducing a hierarchical communication mechanism, H3-DDG effectively models both local and global mutational effects. Experimental results demonstrate state-of-the-art performance on multiple benchmarks. On the SKEMPI v2 dataset, H3-DDG achieves a Pearson correlation of 0.75, improving multi-point mutations prediction by 12.10%. On the challenging BindingGYM dataset, it outperforms Prompt-DDG and BA-DDG by 62.61% and 34.26%, respectively. Ablation and efficiency analyses demonstrate its robustness and scalability, while a case study on SARS-CoV-2 antibodies highlights its practical value in improving binding affinity for therapeutic design.