Ever-increasing numbers of quantitative proteomics data sets constitute an underexploited resource for investigating protein function. Multiprotein complexes often follow consistent trends in these experiments, which could provide insights about thei...
Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large ...
Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interact...
Journal of bioinformatics and computational biology
30803297
The prediction of protein complexes based on the protein interaction network is a fundamental task for the understanding of cellular life as well as the mechanisms underlying complex disease. A great number of methods have been developed to predict p...
Proteins form complexes to accomplish biological functions such as transcription of DNA, translation of mRNA and cell growth. Detection of protein complexes from protein-protein interaction (PPI) networks is the first step for the analysis of biologi...
Methods in molecular biology (Clifton, N.J.)
33215381
Cell-surface adhesion receptors mediate interactions with the extracellular matrix (ECM) to control many fundamental aspects of cell behavior, including cell migration, survival, and proliferation. Integrin adhesion receptors recruit structural and s...
Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits t...
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...