Modeling of an ion channel in its open conformation.
|Abstract||We have modeled the structure of KirBac1.1 in an open state using as a starting point the structure of KirBac1.1 in its closed conformation (Protein Data Bank 1P7B). To test the validity of the open-state model, molecular dynamics simulations in octane, a lipid bilayer mimetic, were carried out. Simulations of the closed conformer were used for comparison purposes. The total simulation time was approximately 138 ns. The initial open model was ref ... [truncated at 450 characters in length]|
|Author||Domene, Carmen; Doyle, Declan A; Vénien-Bryan, Catherine;|
|Subject||Biophysics Burkholderia pseudomallei Crystallography, X-Ray Databases, Protein Glycine Models, Molecular Phenylalanine Potassium Potassium Channels, Inwardly Rectifying Protein Conformation Protein Structure, Secondary methods metabolism chemistry chemistry chemistry chemistry|
Linear motif atlas for phosphorylation-dependent signaling.
|Abstract||Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding ... [truncated at 450 characters in length]|
|Author||Miller, Martin Lee; Jensen, Lars Juhl; Diella, Francesca; et al|
|Subject||14-3-3 Proteins Amino Acid Motifs Animals BRCA1 Protein Consensus Sequence Databases, Protein Humans Phosphorylation Phosphotransferases Phosphotyrosine Protein Binding Signal Transduction src Homology Domains chemistry chemistry chemistry metabolism|
SGC--structural biology and human health: a new approach to publishing structural biology results.
|Author||Lee, Wen Hwa; Atienza-Herrero, Julián; Abagyan, Ruben; et al|
|Subject||Amino Acid Sequence Computational Biology Databases, Protein Genomics Humans Protein Conformation Protein Folding Proteins Publishing Structural Homology, Protein economics methods chemistry classification genetics|
Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models.
|Abstract||The short-chain dehydrogenase/reductase (SDR) superfamily now has over 47 000 members, most of which are distantly related, with typically 20-30% residue identity in pairwise comparisons, making it difficult to obtain an overview of this superfamily. We have therefore developed a family classification system, based upon hidden Markov models (HMMs). To this end, we have identified 314 SDR families, encompassing about 31,900 members. In addition, a ... [truncated at 450 characters in length]|
|Author||Kallberg, Yvonne; Oppermann, Udo; Persson, Bengt;|
|Subject||Animals Archaea Bacteria Cluster Analysis Computational Biology Databases, Protein Eukaryota Genome Humans Markov Chains Mice Oxidoreductases Rats Sequence Alignment enzymology genetics enzymology genetics methods enzymology genetics genetics classification genetics|