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Applications · Chemistry, Physics, and Earth Sciences

Jeet Mohapatra, Nima Dehmamy, Csaba Both, Subhro Das, Tommi Jaakkola

We introduce a novel approach for discovering effective degrees of freedom (DOF) in molecular dynamics simulations by mapping the DOF to approximate symmetries of the energy landscape. Unlike most existing methods, we do not require trajectory data but instead rely on knowledge of the forcefield (energy function) around the initial state. We present a scalable symmetry loss function compatible with existing force-field frameworks and a Hessian-based method efficient for smaller systems. Our approach enables systematic exploration of conformational space by connecting structural dynamics to energy landscape symmetries. We apply our method to two systems, Alanine dipeptide and Chignolin, recovering their known important conformations. Our approach can prove useful for efficient exploration in molecular simulations with potential applications in protein folding and drug discovery.

Deep Learning · Generative Models and Autoencoders

Zhonglin Cao, Mario Geiger, Allan Costa, Danny Reidenbach, Karsten Kreis, Tomas Geffner, Franco Pellegrini, Guoqing Zhou, Emine Kucukbenli

Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art diffusion or flow-based models for conformer generation require significant computational resources. In this work, we build upon flow-matching and propose two mechanisms for accelerating training and inference of generative models for 3D molecular conformer generation. For fast training, we introduce the SO(3)-*Averaged Flow* training objective, which leads to faster convergence to better generation quality compared to conditional optimal transport flow or Kabsch-aligned flow. We demonstrate that models trained using SO(3)-*Averaged Flow* can reach state-of-the-art conformer generation quality. For fast inference, we show that the reflow and distillation methods of flow-based models enable few-steps or even one-step molecular conformer generation with high quality. The training techniques proposed in this work show a path towards highly efficient molecular conformer generation with flow-based models.

Applications · Chemistry, Physics, and Earth Sciences

Benson Chen, Tomasz Danel, Gabriel Dreiman, Patrick McEnaney, Nikhil Jain, Kirill Novikov, Spurti Akki, Joshua L. Turnbull, Virja Pandya, Boris Belotserkovskii 等

DNA-Encoded Libraries (DELs) represent a transformative technology in drug discovery, facilitating the high-throughput exploration of vast chemical spaces. Despite their potential, the scarcity of publicly available DEL datasets presents a bottleneck for the advancement of machine learning methodologies in this domain. To address this gap, we introduce KinDEL, one of the largest publicly accessible DEL datasets and the first one that includes binding poses from molecular docking experiments. Focused on two kinases, Mitogen-Activated Protein Kinase 14 (MAPK14) and Discoidin Domain Receptor Tyrosine Kinase 1 (DDR1), KinDEL includes 81 million compounds, offering a rich resource for computational exploration. Additionally, we provide comprehensive biophysical assay validation data, encompassing both on-DNA and off-DNA measurements, which we use to evaluate a suite of machine learning techniques, including novel structure-based probabilistic models. We hope that our benchmark, encompassing both 2D and 3D structures, will help advance the development of machine learning models for data-driven hit identification using DELs.

Applications · Chemistry and Drug Discovery

Nicholas Gao, Eike Eberhard, Stephan Günnemann

The accuracy of density functional theory hinges on the approximation of non-local contributions to the exchange-correlation (XC) functional. To date, machine-learned and human-designed approximations suffer from insufficient accuracy, limited scalability, or dependence on costly reference data. To address these issues, we introduce Equivariant Graph Exchange Correlation (EG-XC), a novel non-local XC functional based on equivariant graph neural networks (GNNs). Where previous works relied on semi-local functionals or fixed-size descriptors of the density, we compress the electron density into an SO(3)-equivariant nuclei-centered point cloud for efficient non-local atomic-range interactions. By applying an equivariant GNN on this point cloud, we capture molecular-range interactions in a scalable and accurate manner. To train EG-XC, we differentiate through a self-consistent field solver requiring only energy targets. In our empirical evaluation, we find EG-XC to accurately reconstruct `gold-standard' CCSD(T) energies on MD17. On out-of-distribution conformations of 3BPA, EG-XC reduces the relative MAE by 35% to 50%. Remarkably, EG-XC excels in data efficiency and molecular size extrapolation on QM9, matching force fields trained on 5 times more and larger molecules. On identical training sets, EG-XC yields on average 51% lower MAEs.

Applications · Chemistry and Drug Discovery

Hanlin Wu, Yuxuan Song, Jingjing Gong, Ziyao Cao, Yawen Ouyang, Jianbing Zhang, Hao Zhou, Wei-Ying Ma, Jingjing Liu

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song, et al.,2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., 200x speedup (10 v.s. 2000 steps network forwards) compared with previous Diffusion-based methods on MP-20 dataset.

Applications · Chemistry and Drug Discovery

Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng

Antibodies are essential proteins responsible for immune responses in organisms, capable of specifically recognizing antigen molecules of pathogens. Recent advances in generative models have significantly enhanced rational antibody design. However, existing methods mainly create antibodies from scratch without template constraints, leading to model optimization challenges and unnatural sequences. To address these issues, we propose a retrieval-augmented diffusion framework, termed RADAb, for efficient antibody design. Our method leverages a set of structural homologous motifs that align with query structural constraints to guide the generative model in inversely optimizing antibodies according to desired design criteria. Specifically, we introduce a structure-informed retrieval mechanism that integrates these exemplar motifs with the input backbone through a novel dual-branch denoising module, utilizing both structural and evolutionary information. Additionally, we develop a conditional diffusion model that iteratively refines the optimization process by incorporating both global context and local evolutionary conditions. Our approach is agnostic to the choice of generative models. Empirical experiments demonstrate that our method achieves state-of-the-art performance in multiple antibody inverse folding and optimization tasks, offering a new perspective on biomolecular generative models.

Applications · Chemistry and Drug Discovery

Yi Zhou, Yilai Li, Jing Yuan, Quanquan Gu

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of around 40k protein density maps at various resolutions. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CryoFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

Applications · Chemistry and Drug Discovery

Jiaqi Guan, Jiahan Li, Xiangxin Zhou, Xingang Peng, Sheng Wang, Yunan Luo, Jian Peng, Jianzhu Ma

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding to the same target protein tend to adopt similar poses, we propose \textsc{GroupBind}, a novel molecular docking framework that simultaneously considers multiple ligands docking to a protein. This is achieved by introducing an interaction layer for the group of ligands and a triangle attention module for embedding protein-ligand and group-ligand pairs. By integrating our approach with diffusion based docking model, we set a new state-of-the-art performance on the PDBBind blind docking benchmark, demonstrating the effectiveness of our paradigm in enhancing molecular docking accuracy.

Applications · Chemistry and Drug Discovery

Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, Qiang Liu, Feng Zhou, Liang Wang, Jianzhu Ma

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, we propose to use generative modeling for SBDD considering conformational changes of protein pockets. We curate a dataset of apo and multiple holo states of protein-ligand complexes, simulated by molecular dynamics, and propose a full-atom flow model (and a stochastic version), named DynamicFlow, that learns to transform apo pockets and noisy ligands into holo pockets and corresponding 3D ligand molecules. Our method uncovers promising ligand molecules and corresponding holo conformations of pockets. Additionally, the resultant holo-like states provide superior inputs for traditional SBDD approaches, playing a significant role in practical drug discovery.

Applications · Chemistry and Drug Discovery

Shaorong Chen, Jun Xia, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z Li

Proteomics is the large-scale study of proteins. Tandem mass spectrometry, as the only high-throughput technique for protein sequence identification, plays a pivotal role in proteomics research. One of the long-standing challenges in this field is peptide identification, which entails determining the specific peptide (sequence of amino acids) that corresponds to each observed mass spectrum. The conventional approach involves database searching, wherein the observed mass spectrum is scored against a pre-constructed peptide database. However, the reliance on pre-existing databases limits applicability in scenarios where the peptide is absent from existing databases. Such circumstances necessitate \emph{de novo} peptide sequencing, which derives peptide sequence solely from input mass spectrum, independent of any peptide database. Despite ongoing advancements in \emph{de novo} peptide sequencing, its performance still has considerable room for improvement, which limits its application in large-scale experiments. In this study, we introduce a novel \textbf{Re}trieval-based \emph{De \textbf{Novo}} peptide sequencing methodology, termed \textbf{ReNovo}, which draws inspiration from database search methods. Specifically, by constructing a datastore from training data, ReNovo can retrieve information from the datastore during the inference stage to conduct retrieval-based inference, thereby achieving improved performance. This innovative approach enables ReNovo to effectively combine the strengths of both methods: utilizing the assistance of the datastore while also being capable of predicting novel peptides that are not present in pre-existing databases. A series of experiments have confirmed that ReNovo outperforms state-of-the-art models across multiple widely-used datasets, incurring only minor storage and time consumption, representing a significant advancement in proteomics. Supplementary materials include the code.

Applications · Chemistry and Drug Discovery

Yinkai Wang, Xiaohui Chen, Liping Liu, Soha Hassoun

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Applications · Chemistry and Drug Discovery

Minghao Xu, Yunteng Geng, Yihang Zhang, Ling Yang, Jian Tang, Wentao Zhang

Glycans are basic biomolecules and perform essential functions within living organisms. The rapid increase of functional glycan data provides a good opportunity for machine learning solutions to glycan understanding. However, there still lacks a standard machine learning benchmark for glycan property and function prediction. In this work, we fill this blank by building a comprehensive benchmark for Glycan Machine Learning (GlycanML). The GlycanML benchmark consists of diverse types of tasks including glycan taxonomy prediction, glycan immunogenicity prediction, glycosylation type prediction, and protein-glycan interaction prediction. Glycans can be represented by both sequences and graphs in GlycanML, which enables us to extensively evaluate sequence-based models and graph neural networks (GNNs) on benchmark tasks. Furthermore, by concurrently performing eight glycan taxonomy prediction tasks, we introduce the GlycanML-MTL testbed for multi-task learning (MTL) algorithms. Also, we evaluate how taxonomy prediction can boost other three function prediction tasks by MTL. Experimental results show the superiority of modeling glycans with multi-relational GNNs, and suitable MTL methods can further boost model performance. We provide all datasets and source codes at https://github.com/GlycanML/GlycanML and maintain a leaderboard at https://GlycanML.github.io/project

Applications · Chemistry and Drug Discovery

Shuai Zhang, Junfeng Fang, Xuqiang Li, Hongxin Xiang, Jun Xia, Ye Wei, Wenjie Du, Yang Wang

Molecular relational learning (MRL) seeks to understand the interaction behaviors between molecules, a pivotal task in domains such as drug discovery and materials science. Recently, extracting core substructures and modeling their interactions have emerged as mainstream approaches within machine learning-assisted methods. However, these methods still exhibit some limitations, such as insufficient consideration of molecular interactions or capturing substructures that include excessive noise, which hampers precise core substructure extraction.To address these challenges, we present an integrated dynamic framework called Iterative Substructure Extraction (ISE). ISE employs the Expectation-Maximization (EM) algorithm for MRL tasks, where the core substructures of interacting molecules are treated as latent variables and model parameters, respectively. Through iterative refinement, ISE gradually narrows the interactions from the entire molecular structures to just the core substructures.Moreover, to ensure the extracted substructures are concise and compact, we propose the Interactive Graph Information Bottleneck (IGIB) theory, which focuses on capturing the most influential yet minimal interactive substructures. In summary, our approach, guided by the IGIB theory, achieves precise substructure extraction within the ISE framework and is encapsulated in the IGIB-ISE}Extensive experiments validate the superiority of our model over state-of-the-art baselines across various tasks in terms of accuracy, generalizability, and interpretability.

Applications · Chemistry and Drug Discovery

Daniel Levy, Siba Smarak Panigrahi, Sékou-Oumar Kaba, Qiang Zhu, Kin Long Kelvin Lee, Mikhail Galkin, Santiago Miret, Siamak Ravanbakhsh

Generating novel crystalline materials has potential to lead to advancements in fields such as electronics, energy storage, and catalysis. The defining characteristic of crystals is their symmetry, which plays a central role in determining their physical properties. However, existing crystal generation methods either fail to generate materials that display the symmetries of real-world crystals, or simply replicate the symmetry information from examples in a database. To address this limitation, we propose SymmCD, a novel diffusion-based generative model that explicitly incorporates crystallographic symmetry into the generative process. We decompose crystals into two components and learn their joint distribution through diffusion: 1) the asymmetric unit, the smallest subset of the crystal which can generate the whole crystal through symmetry transformations, and; 2) the symmetry transformations needed to be applied to each atom in the asymmetric unit. We also use a novel and interpretable representation for these transformations, enabling generalization across different crystallographic symmetry groups. We showcase the competitive performance of SymmCD on a subset of the Materials Project, obtaining diverse and valid crystals with realistic symmetries and predicted properties.

Applications · Chemistry and Drug Discovery

Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao

Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in analyzing biological sequences, existing approaches fail to account for the hierarchical nature of mRNA's codon structure. We introduce Hierarchical Encoding for mRNA Language Modeling (HELM), a novel pre-training strategy that incorporates codon-level hierarchical structure into language model training. HELM modulates the loss function based on codon synonymity, aligning the model's learning process with the biological reality of mRNA sequences. We evaluate HELM on diverse mRNA datasets and tasks, demonstrating that HELM outperforms standard language model pre-training as well as existing foundation model baselines on six diverse downstream property prediction tasks and an antibody region annotation tasks on average by around 8%. Additionally, HELM enhances the generative capabilities of language model, producing diverse mRNA sequences that better align with the underlying true data distribution compared to non-hierarchical baselines.

Applications · Chemistry and Drug Discovery

Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne Carpenter, Meng Jiang, Shantanu Singh

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream applications: molecular property prediction against up to 27 baseline methods across four datasets, plus zero-shot molecule-morphology matching. The code and model are available at https://github.com/liugangcode/InfoAlign.

Applications · Chemistry and Drug Discovery

Xinyou Wang, Zaixiang Zheng, Fei YE, Dongyu Xue, Shujian Huang, Quanquan Gu

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities.In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures.To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer.By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals.We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models.Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach.Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs.

Applications · Chemistry and Drug Discovery

Gabriel Claude Jean Ducrocq, Lukas Grunewald, Sebastian Westenhoff, Fredrik Lindsten

The three-dimensional structure of proteins plays a crucial role in determining their function. Protein structure prediction methods, like AlphaFold, offer rapid access to a protein’s structure. However, large protein complexes cannot be reliably predicted, and proteins are dynamic, making it important to resolve their full conformational distribution. Single-particle cryo-electron microscopy (cryo-EM) is a powerful tool for determining the structures of large protein complexes. Importantly, the numerous images of a given protein contain underutilized information about conformational heterogeneity. These images are very noisy projections of the protein, and traditional methods for cryo-EM reconstruction are limited to recovering only one or a few consensus conformations.In this paper, we introduce cryoSPHERE, which is a deep learning method that uses a nominal protein structure (e.g., from AlphaFold) as input, learns how to divide it into segments, and moves these segments as approximately rigid bodies to fit the different conformations present in the cryo-EM dataset. This approach provides enough constraints to enable meaningful reconstructions of single protein structural ensembles. We demonstrate this with two synthetic datasets featuring varying levels of noise, as well as two real dataset. We show that cryoSPHERE is very resilient to the high levels of noise typically encountered in experiments, where we see consistent improvements over the current state-of-the-art for heterogeneous reconstruction.

Applications · Chemistry and Drug Discovery

Xiuyuan Hu, Guoqing Liu, Can Chen, Yang Zhao, Hao Zhang, Xue Liu

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer.

Applications · Chemistry and Drug Discovery

Jingjie Zhang, Hanqun Cao, Zijun Gao, Xiaorui Wang, Chunbin Gu

Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused and individual kinase-targeted approaches. Individual kinase-targeted methods have gained prominence for their ability to explore a broader protein space and provide more precise target information for kinase inhibitors. However, most existing individual kinase-based approaches focus solely on sequence inputs, neglecting crucial structural information. To address this limitation, we introduce SAGEPhos (Structure-aware kinAse-substrate bio-coupled and bio-auGmented nEtwork for Phosphorylation site prediction), a novel framework that modifies the semantic space of main protein inputs using auxiliary inputs at two distinct modality levels. At the inter-modality level, SAGEPhos introduces a Bio-Coupled Modal Fusion method, distilling essential kinase sequence information to refine task-oriented local substrate feature space, creating a shared semantic space that captures crucial kinase-substrate interaction patterns. Within the substrate's intra-modality domain, it focuses on Bio-Augmented Fusion, emphasizing 2D local sequence information while selectively incorporating 3D spatial information from predicted structures to complement the sequence space. Moreover, to address the lack of structural information in current datasets, we contribute a new, refined phosphorylation site prediction dataset, which incorporates crucial structural elements and will serve as a new benchmark for the field. Experimental results demonstrate that SAGEPhos significantly outperforms baseline methods, notably achieving almost 10\% and 12\% improvements in prediction accuracy and AUC-ROC, respectively. We further demonstrate our algorithm's robustness and generalization through stable results across varied data partitions and significant improvements in zero-shot scenarios. These results underscore the effectiveness of constructing a larger and more precise protein space in advancing the state-of-the-art in phosphorylation site prediction. We release the SAGEPhos models and code at https://github.com/ZhangJJ26/SAGEPhos.