CyberSec Research

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 go from raw experimental data to 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 protein 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.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference Optimization (DPO) to fine-tune an inverse folding model using feedback from a protein folding model. Given a target protein structure, we begin by sampling candidate sequences from the inverse-folding model, then predict the three-dimensional structure of each sequence with the folding model to generate pairwise structural-preference labels. These labels are used to fine-tune the inverse-folding model under the DPO objective. Our results on the CATH 4.2 test set demonstrate that DPO fine-tuning not only improves sequence recovery of baseline models but also leads to a significant improvement in average TM-Score from 0.77 to 0.81, indicating enhanced structure similarity. Furthermore, iterative application of our DPO-based method on challenging protein structures yields substantial gains, with an average TM-Score increase of 79.5\% with regard to the baseline model. This work establishes a promising direction for enhancing protein sequence design ability from structure feedback by effectively utilizing preference optimization.

In this study, the distributions of protein folding classes of experimentally determined structures from a legacy dataset and a comprehensive database SCOPe are modeled with precise geometric objects as convex polytopes in the high-dimensional amino acid composition space. This is a follow-up of a previous non-statistical, geometry-motivated modeling of protein classes with ellipsoidal models, which are superseded presently in three important respects: (1) as a paradigm shift descriptive 'distribution models' of experimental data are de-coupled from, and serves as the basis for, future potential predictive 'domain models' generalizable to proteins in the same structure class for which the 3-dimensional structures have yet to be determined experimentally, (2) the geometric and analytic characteristics of class distributions are obtained via exact computational geometry calculations, and (3) the full data from a comprehensive database are included in such calculations, eschewing training set selection and biases. In contrast to statistical inference and machine-learning approaches, the analytical, non-statistical geometry models of protein class distributions demonstrated in this study, complete with precise information on the size of class distributions and their relative disposition in the high-dimensional space, and intended not principally for prediction but as accurate description of the complex relationships between amino acid composition and protein classes, suggest that they may ultimately be useful adjuncts for validating sequence-based methods for predicting protein structures and contribute to the mechanistic understanding of secondary structure formation and the folding of polypeptide chains into 3-dimensional conformation of functional protein molecules.

Climate change is a major threat to crop potential and is characterized by both long-term shifts in temperature and precipitation patterns as well as increased occurrence of extreme weather events, these extreme weather events are the most immediate and intractable threat to agriculture. Crop resilience in the face of stress depends upon the speed and effectiveness with which plants and cropping systems sense and respond to that stress. A variety of agronomic practices including breeding, exogenous inputs (nutrients, water, biostimulants and others) and shifts in cultivation practice have been used to influence plant stress response to achieve the goal of increased plant and cropping system resilience. Traditional breeding is a powerful tool that has resulted in stable and long-term cultivar improvements but is often too slow and complex to meet the diverse, complex and unpredictable challenges of climate induced stresses. Increased inputs (water, nutrients, pesticides etc.) and management strategies (cropping system choice, soil management etc.) can alleviate stress but are often constrained by cost and availability of inputs. Exogenous biostimulants, microbials and plant hormones have shown great promise as mechanisms to optimize natural plant resilience resulting in immediate but non-permanent improvements in plant responses to climate induced stresses. The failure to modernize regulatory frameworks for the use of biostimulants in agriculture will constrain the development of safe effective tools and deprive growers of means to respond to the vagaries of climate change. Here we discuss the scientific rationale for eliminating the regulatory barriers that constrain the potential for biostimulants or products that modulate plant regulatory networks to address climate change challenges and propose a framework for enabling legislation to strengthen cropping system resilience.

Hybrid quantum-classical machine learning offers a path to leverage noisy intermediate-scale quantum (NISQ) devices for drug discovery, but optimal model architectures remain unclear. We systematically optimize the quantum-classical bridge architecture for generative adversarial networks (GANs) in molecular discovery using multi-objective Bayesian optimization. Our optimized model (BO-QGAN) significantly improves performance, achieving a 2.27-fold higher Drug Candidate Score (DCS) than prior quantum-hybrid benchmarks and 2.21-fold higher than the classical baseline, using over 60% fewer parameters. Key findings favor layering multiple (3-4) shallow (4-8 qubit) quantum circuits sequentially, while classical architecture shows less sensitivity above a minimum capacity. This work provides the first empirically grounded architectural guidelines for hybrid models, enabling more effective integration of current quantum computers into pharmaceutical research pipelines.

Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of the problem: multiple diverse sequences can fold into the same structure. This motivates the need for a generative model capable of designing diverse sequences while preserving structural consistency. To address this trade-off, we introduce ProtInvTree, the first reward-guided tree-search framework for protein inverse folding. ProtInvTree reformulates sequence generation as a deliberate, step-wise decision-making process, enabling the exploration of multiple design paths and exploitation of promising candidates through self-evaluation, lookahead, and backtracking. We propose a two-stage focus-and-grounding action mechanism that decouples position selection and residue generation. To efficiently evaluate intermediate states, we introduce a jumpy denoising strategy that avoids full rollouts. Built upon pretrained protein language models, ProtInvTree supports flexible test-time scaling by expanding the search depth and breadth without retraining. Empirically, ProtInvTree outperforms state-of-the-art baselines across multiple benchmarks, generating structurally consistent yet diverse sequences, including those far from the native ground truth.

Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance performance in specialized tasks. In this work, we introduce $\textbf{Protap}$, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Specifically, Protap covers five applications: three general tasks and two novel specialized tasks, i.e., enzyme-catalyzed protein cleavage site prediction and targeted protein degradation, which are industrially relevant yet missing from existing benchmarks. For each application, Protap compares various domain-specific models and general architectures under multiple pretraining settings. Our empirical studies imply that: (i) Though large-scale pretraining encoders achieve great results, they often underperform supervised encoders trained on small downstream training sets. (ii) Incorporating structural information during downstream fine-tuning can match or even outperform protein language models pretrained on large-scale sequence corpora. (iii) Domain-specific biological priors can enhance performance on specialized downstream tasks. Code and datasets are publicly available at https://github.com/Trust-App-AI-Lab/protap.

The de novo generation of drug-like molecules capable of inducing desirable phenotypic changes is receiving increasing attention. However, previous methods predominantly rely on expression profiles to guide molecule generation, but overlook the perturbative effect of the molecules on cellular contexts. To overcome this limitation, we propose SmilesGEN, a novel generative model based on variational autoencoder (VAE) architecture to generate molecules with potential therapeutic effects. SmilesGEN integrates a pre-trained drug VAE (SmilesNet) with an expression profile VAE (ProfileNet), jointly modeling the interplay between drug perturbations and transcriptional responses in a common latent space. Specifically, ProfileNet is imposed to reconstruct pre-treatment expression profiles when eliminating drug-induced perturbations in the latent space, while SmilesNet is informed by desired expression profiles to generate drug-like molecules. Our empirical experiments demonstrate that SmilesGEN outperforms current state-of-the-art models in generating molecules with higher degree of validity, uniqueness, novelty, as well as higher Tanimoto similarity to known ligands targeting the relevant proteins. Moreover, we evaluate SmilesGEN for scaffold-based molecule optimization and generation of therapeutic agents, and confirmed its superior performance in generating molecules with higher similarity to approved drugs. SmilesGEN establishes a robust framework that leverages gene signatures to generate drug-like molecules that hold promising potential to induce desirable cellular phenotypic changes.

Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved promising results. However, the increasing availability of diverse LLMs and molecular structure encoders has significantly expanded the model space, presenting major challenges for benchmarking. Currently, there is no LLM framework that supports both flexible molecular input formats and dynamic architectural switching. To address these challenges, reduce redundant coding, and ensure fair model comparison, we propose ModuLM, a framework designed to support flexible LLM-based model construction and diverse molecular representations. ModuLM provides a rich suite of modular components, including 8 types of 2D molecular graph encoders, 11 types of 3D molecular conformation encoders, 7 types of interaction layers, and 7 mainstream LLM backbones. Owing to its highly flexible model assembly mechanism, ModuLM enables the dynamic construction of over 50,000 distinct model configurations. In addition, we provide comprehensive results to demonstrate the effectiveness of ModuLM in supporting LLM-based MRL tasks.

Protein sequence design methods have demonstrated strong performance in sequence generation for de novo protein design. However, as the training objective was sequence recovery, it does not guarantee designability--the likelihood that a designed sequence folds into the desired structure. To bridge this gap, we redefine the training objective by steering sequence generation toward high designability. To do this, we integrate Direct Preference Optimization (DPO), using AlphaFold pLDDT scores as the preference signal, which significantly improves the in silico design success rate. To further refine sequence generation at a finer, residue-level granularity, we introduce Residue-level Designability Preference Optimization (ResiDPO), which applies residue-level structural rewards and decouples optimization across residues. This enables direct improvement in designability while preserving regions that already perform well. Using a curated dataset with residue-level annotations, we fine-tune LigandMPNN with ResiDPO to obtain EnhancedMPNN, which achieves a nearly 3-fold increase in in silico design success rate (from 6.56% to 17.57%) on a challenging enzyme design benchmark.

Deep learning-based prediction of protein-ligand complexes has advanced significantly with the development of architectures such as AlphaFold3, Boltz-1, Chai-1, Protenix, and NeuralPlexer. Multiple sequence alignment (MSA) has been a key input, providing coevolutionary information critical for structural inference. However, recent benchmarks reveal a major limitation: these models often memorize ligand poses from training data and perform poorly on novel chemotypes or dynamic binding events involving substantial conformational changes in binding pockets. To overcome this, we introduced a state-aware protein-ligand prediction strategy leveraging purified sequence subsets generated by AF-ClaSeq - a method previously developed by our group. AF-ClaSeq isolates coevolutionary signals and selects sequences that preferentially encode distinct structural states as predicted by AlphaFold2. By applying MSA-derived conformational restraints, we observed significant improvements in predicting ligand poses. In cases where AlphaFold3 previously failed-producing incorrect ligand placements and associated protein conformations-we were able to correct the predictions by using sequence subsets corresponding to the relevant functional state, such as the inactive form of an enzyme bound to a negative allosteric modulator. We believe this approach represents a powerful and generalizable strategy for improving protein-ligand complex predictions, with potential applications across a broad range of molecular modeling tasks.

Background: Platelet proteomics offers valuable insights for clinical research, yet isolating high-purity platelets remains a challenge. Current methods often lead to contamination or platelet loss, compromising data quality and reproducibility. Objectives: This study aimed to optimize a platelet isolation technique that yields high-purity samples with minimal loss and to identify the most effective mass spectrometry-based proteomic method for analyzing platelet proteins with optimal coverage and sensitivity. Methods: We refined an isolation protocol by adjusting centrifugation time to reduce blood volume requirements while preserving platelet yield and purity. Using this optimized method, we evaluated three proteomic approaches: Label-free Quantification with Data-Independent Acquisition (LFQ-DIA), Label-free Quantification with Data-Dependent Acquisition (LFQ-DDA), and Tandem Mass Tag labeling with DDA (TMT-DDA). Results: LFQ-DIA demonstrated superior protein coverage and sensitivity compared to LFQ-DDA and TMT-DDA. The refined isolation protocol effectively minimized contamination and platelet loss. Additionally, age-related differences in platelet protein composition were observed, highlighting the importance of using age-matched controls in biomarker discovery studies. Conclusions: The optimized platelet isolation protocol provides a cost-effective and reliable method for preparing high-purity samples for proteomics. LFQ-DIA is the most suitable approach for comprehensive platelet protein analysis. Age-related variation in platelet proteomes underscores the need for demographic matching in clinical proteomic research.

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative modeling, particularly denoising diffusion models, have enabled efficient accurate protein structure prediction and conformation sampling by learning distributions over crystallographic structures. However, effectively integrating physical supervision into these data-driven approaches remains challenging, as standard energy-based objectives often lead to intractable optimization. In this paper, we introduce Energy-based Alignment (EBA), a method that aligns generative models with feedback from physical models, efficiently calibrating them to appropriately balance conformational states based on their energy differences. Experimental results on the MD ensemble benchmark demonstrate that EBA achieves state-of-the-art performance in generating high-quality protein ensembles. By improving the physical plausibility of generated structures, our approach enhances model predictions and holds promise for applications in structural biology and drug discovery.

In real-world drug design, molecule optimization requires selectively improving multiple molecular properties up to pharmaceutically relevant levels, while maintaining others that already meet such criteria. However, existing computational approaches and instruction-tuned LLMs fail to capture such nuanced property-specific objectives, limiting their practical applicability. To address this, we introduce C-MuMOInstruct, the first instruction-tuning dataset focused on multi-property optimization with explicit, property-specific objectives. Leveraging C-MuMOInstruct, we develop GeLLMO-Cs, a series of instruction-tuned LLMs that can perform targeted property-specific optimization. Our experiments across 5 in-distribution and 5 out-of-distribution tasks show that GeLLMO-Cs consistently outperform strong baselines, achieving up to 126% higher success rate. Notably, GeLLMO-Cs exhibit impressive 0-shot generalization to novel optimization tasks and unseen instructions. This offers a step toward a foundational LLM to support realistic, diverse optimizations with property-specific objectives. C-MuMOInstruct and code are accessible through https://github.com/ninglab/GeLLMO-C.

The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and biomolecular interactions. However, these environments' extensive structural and chemical variability makes them challenging to model, and such representations remain under-explored. In this work, we propose a novel representation for a local protein environment derived from the intermediate features of atomistic foundation models (AFMs). We demonstrate that this embedding effectively captures both local structure (e.g., secondary motifs), and chemical features (e.g., amino-acid identity and protonation state). We further show that the AFM-derived representation space exhibits meaningful structure, enabling the construction of data-driven priors over the distribution of biomolecular environments. Finally, in the context of biomolecular NMR spectroscopy, we demonstrate that the proposed representations enable a first-of-its-kind physics-informed chemical shift predictor that achieves state-of-the-art accuracy. Our results demonstrate the surprising effectiveness of atomistic foundation models and their emergent representations for protein modeling beyond traditional molecular simulations. We believe this will open new lines of work in constructing effective functional representations for protein environments.

Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities. In this work, we introduce CFP-Gen, a novel diffusion language model for Combinatorial Functional Protein GENeration. CFP-Gen facilitates the de novo protein design by integrating multimodal conditions with functional, sequence, and structural constraints. Specifically, an Annotation-Guided Feature Modulation (AGFM) module is introduced to dynamically adjust the protein feature distribution based on composable functional annotations, e.g., GO terms, IPR domains and EC numbers. Meanwhile, the Residue-Controlled Functional Encoding (RCFE) module captures residue-wise interaction to ensure more precise control. Additionally, off-the-shelf 3D structure encoders can be seamlessly integrated to impose geometric constraints. We demonstrate that CFP-Gen enables high-throughput generation of novel proteins with functionality comparable to natural proteins, while achieving a high success rate in designing multifunctional proteins. Code and data available at https://github.com/yinjunbo/cfpgen.