Related papers: Inferring interaction partners from protein sequen…
To construct models of large, multivariate complex systems, such as those in biology, one needs to constrain which variables are allowed to interact. This can be viewed as detecting "local" structures among the variables. In the context of…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…
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…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
Although instantaneous interactions are unphysical, a large variety of maximum entropy statistical inference methods match the model-inferred and the empirically-measured equal-time correlation functions. Focusing on collective motion of…
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…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
Protein-protein interaction extraction is the key precondition of the construction of protein knowledge network, and it is very important for the research in the biomedicine. This paper extracted directional protein-protein interaction from…
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods…
Protein-protein interaction (PPI) prediction is an instrumental means in elucidating the mechanisms underlying cellular operations, holding significant practical implications for the realms of pharmaceutical development and clinical…
Interacting systems are ubiquitous in nature and engineering, ranging from particle dynamics in physics to functionally connected brain regions. These interacting systems can be modeled by graphs where edges correspond to the interactions…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature collective correlations in their amino-acid usage, and they…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…