Dynamic network analysis improves protein 3D structural classification [PDF]
arXiv, 2021 Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3D structural features. We recently proposed PSC approaches that model protein 3D structures as protein structure networks (PSNs) and analyze PSN-based protein features, which
arxiv
A novel methodology on distributed representations of proteins using their interacting ligands [PDF]
Bioinformatics 2018, 2018 The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand based approach can be utilized in ...
arxiv +1 more source
Protein Structure Prediction Using Basin-Hopping
, 2008 Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins.
David J. Wales +4 more
core +2 more sources
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review [PDF]
, 2011 During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global ...
Daniel V. Veres +8 more
core +4 more sources
Structure of the AAA protein Msp1 reveals mechanism of mislocalized membrane protein extraction. [PDF]
, 2020 The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization.
Myasnikov, Alexander +3 more
core +2 more sources
Crystal structure of 1-(2,4-dihydroxy-6-methylphenyl)ethanone
Acta Crystallographica Section E: Crystallographic Communications, 2015 The title compound, C9H10O3, is a bioactive secondary metabolite, isolated from the endophytic fungus Nodulisporium sp. The compound exhibits an intramolecular O—H...O hydrogen bond between the phenolic H atom and the carbonyl O atom of the adjacent ...
Samran Prabpai, Palangpon Kongsaeree
doaj +1 more source
Virtual Identification of Essential Proteins Within the Protein Interaction Network of Yeast [PDF]
, 2005 Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability.
arxiv +1 more source
Towards Reliable Automatic Protein Structure Alignment
, 2013 A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local ...
A. Caprara +31 more
core +1 more source
RosettaBackrub--a web server for flexible backbone protein structure modeling and design. [PDF]
, 2010 The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling.
Friedland, Gregory F +4 more
core +2 more sources
Nuclear VPS35 attenuates NHEJ repair by sequestering Ku protein
Molecular MedicineVacuolar protein sorting-associated protein 35 (VPS35), a pivotal constituent of the retromer complex, mediates the retrograde trafficking of endosomal cargoes in the cytoplasm.
Luping Zhang +12 more
doaj +1 more source