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Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…
An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of…
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…
Mutual information is a general statistical dependency measure which has found applications in representation learning, causality, domain generalization and computational biology. However, mutual information estimators are typically…
In analysis of multi-component complex systems, such as neural systems, identifying groups of units that share similar functionality will aid understanding of the underlying structures of the system. To find such a grouping, it is useful to…
We present a new mixed-integer programming (MIP) approach for offline multiple change-point detection by casting the problem as a globally optimal piecewise linear (PWL) fitting problem. Our main contribution is a family of strengthened MIP…
This paper describes a new library for learning Bayesian networks from data containing discrete and continuous variables (mixed data). In addition to the classical learning methods on discretized data, this library proposes its algorithm…
Recently, two methods have shown outstanding performance for clustering images and jointly learning the feature representation. The first, called Information Maximiz-ing Self-Augmented Training (IMSAT), maximizes the mutual information…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
We present an algorithm for computing melting points by autonomously learning from coexistence simulations in the NPT ensemble. Given the interatomic interaction model, the method makes decisions regarding the number of atoms and…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
We transform join ordering into a mixed integer linear program (MILP). This allows to address query optimization by mature MILP solver implementations that have evolved over decades and steadily improved their performance. They offer…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…