Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors

Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are often slow and costly. The advent of deep learning-based approaches has shown significant promise, offering increases in both accuracy and efficiency. Building upon the foundational work of FABind, a model designed with a focus on speed and accuracy, we present FABind+, an enhanced iteration that largely boosts the performance of its predecessor. We identify pocket prediction as a critical bottleneck in molecular docking and propose a novel methodology that significantly refines pocket prediction, thereby streamlining the docking process. Furthermore, we introduce modifications to the docking module to enhance its pose generation capabilities. In an effort to bridge the gap with conventional sampling/generative methods, we incorporate a simple yet effective sampling technique coupled with a confidence model, requiring only minor adjustments to the regression framework of FABind. Experimental results and analysis reveal that FABind+ remarkably outperforms the original FABind, achieves competitive state-of-the-art performance, and delivers insightful modeling strategies. This demonstrates FABind+ represents a substantial step forward in molecular docking and drug discovery. Our code is in https://github.com/QizhiPei/FABind.

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in \url{https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling}.

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{https://github.com/QizhiPei/BioT5}{Github}$.

FABind: Fast and Accurate Protein-Ligand Binding

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at $\href{https://github.com/QizhiPei/FABind}{Github}$.

SMT-DTA: Improving Drug-Target Affinity Prediction with Semi-supervised Multi-task Training

Drug-Target Affinity (DTA) prediction is an essential task for drug discovery and pharmaceutical research. Accurate predictions of DTA can greatly benefit the design of new drug. As wet experiments are costly and time consuming, the supervised data for DTA prediction is extremely limited. This seriously hinders the application of deep learning based methods, which require a large scale of supervised data. To address this challenge and improve the DTA prediction accuracy, we propose a framework with several simple yet effective strategies in this work: (1) a multi-task training strategy, which takes the DTA prediction and the masked language modeling (MLM) task on the paired drug-target dataset; (2) a semi-supervised training method to empower the drug and target representation learning by leveraging large-scale unpaired molecules and proteins in training, which differs from previous pre-training and fine-tuning methods that only utilize molecules or proteins in pre-training; and (3) a cross-attention module to enhance the interaction between drug and target representation. Extensive experiments are conducted on three real-world benchmark datasets: BindingDB, DAVIS and KIBA. The results show that our framework significantly outperforms existing methods and achieves state-of-the-art performances, e.g., $0.712$ RMSE on BindingDB IC$_{50}$ measurement with more than $5\%$ improvement than previous best work. In addition, case studies on specific drug-target binding activities, drug feature visualizations, and real-world applications demonstrate the great potential of our work. The code and data are released at https://github.com/QizhiPei/SMT-DTA