Related papers: Simultaneous identification of specifically intera…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Motivation. Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains very challenging…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
The field of protein-ligand pose prediction has seen significant advances in recent years, with machine learning-based methods now being commonly used in lieu of classical docking methods or even to predict all-atom protein-ligand complex…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract "direct" correlations between distant sites that are latent in "indirect" correlations observed in a protein multiple-sequence…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…
Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…
Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose…