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Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
Understanding protein-metal interactions is central to structural biology, with metal ions being vital for catalysis, stability, and signal transduction. Predicting metal-binding residues and metal types remains challenging due to the…
Recent advances in AI for science have highlighted the power of contrastive learning in bridging heterogeneous biological data modalities. Building on this paradigm, we propose HIPPO (HIerarchical Protein-Protein interaction prediction…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein…
Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Complex systems, such as economic, social, biological, and ecological systems, usually feature interactions not only between pairwise entities but also among three or more entities. These multi-entity interactions are known as higher-order…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…