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Lipophilicity is one of the factors determining the permeability of the cell membrane to a drug molecule. Hence, accurate lipophilicity prediction is an essential step in the development of new drugs. In this paper, we introduce a novel…

Peptide design plays a pivotal role in therapeutics, allowing brand new possibility to leverage target binding sites that are previously undruggable. Most existing methods are either inefficient or only concerned with the target-agnostic…

Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence…

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…

Functional peptides have the potential to treat a variety of diseases. Their good therapeutic efficacy and low toxicity make them ideal therapeutic agents. Artificial intelligence-based computational strategies can help quickly identify new…

Peptide classification tasks, such as predicting toxicity and HIV inhibition, are fundamental to bioinformatics and drug discovery. Traditional approaches rely heavily on handcrafted encodings of one-dimensional (1D) peptide sequences,…

Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration…

Macrocyclic peptides are an emerging modality that combines biologics-like affinity with small-molecule-like developability, but their vast combinatorial space and multi-parameter objectives make lead optimization slow and challenging.…

In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…

Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…

Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of…

Drug discovery is a highly complicated process, and it is unfeasible to fully commit it to the recently developed molecular generation methods. Deep learning-based lead optimization takes expert knowledge as a starting point, learning from…

Among these, D-peptides are resistant to proteolysis, exhibit greater in vivo stability, and are easier to synthesize. Despite advances in deep learning for peptide discovery, the scarcity of natural D-protein data limits the transfer of…

Peptides are biomolecules comprised of amino acids that play an important role in our body. In recent years, peptides have received extensive attention in drug design and synthesis, and peptide prediction tasks help us better search for…

Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide…

Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…

Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…