Related papers: Network and Sequence-Based Prediction of Protein-P…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user…
Protein-protein interaction networks associated with diseases have gained prominence as an area of research. We investigate algebraic and topological indices for protein-protein interaction networks of 11 human cancers derived from the…
Predicting interactions between proteins is one of the most important yet challenging problems in structural bioinformatics. Intrinsically, potential function sites in protein surfaces are determined by both geometric and chemical features.…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and…
Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins…
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…
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…
Close human-robot cooperation is a key enabler for new developments in advanced manufacturing and assistive applications. Close cooperation require robots that can predict human actions and intent, and understand human non-verbal cues.…
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…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…