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SOSUI

About: SOSUI is a research topic. Over the lifetime, 63 publications have been published within this topic receiving 36856 citations.


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Journal ArticleDOI
TL;DR: A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised and its simplicity and its graphic nature make it a very useful tool for the evaluation of protein structures.

21,921 citations

Journal ArticleDOI
TL;DR: A new membrane protein topology prediction method, TMHMM, based on a hidden Markov model is described and validated, and it is discovered that proteins with N(in)-C(in) topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans, where the large number of 7TM receptors increases the counts for N(out)-C-in topologies.

11,453 citations

Journal ArticleDOI
TL;DR: The system SOSUI for the discrimination of membrane proteins and soluble ones together with the prediction of transmembrane helices was developed, in which the accuracy of the classification of proteins was 99% and the corresponding value for the trans Membrane helix prediction was 97%.
Abstract: UNLABELLED The system SOSUI for the discrimination of membrane proteins and soluble ones together with the prediction of transmembrane helices was developed, in which the accuracy of the classification of proteins was 99% and the corresponding value for the transmembrane helix prediction was 97%. AVAILABILITY The system SOSUI is available through internet access: http://www.tuat.ac.jp/mitaku/sosui/. CONTACT sosui@biophys.bio.tuat. ac.jp.

1,871 citations

Journal ArticleDOI
TL;DR: Detailed statistical analyses of integral membrane proteins of the helix‐bundle class from eubacterial, archaean, and eukaryotic organisms for which genome‐wide sequence data are available suggest that uni‐cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegans and Homo sapiens have a slight preference for proteins with seven transmemBRane segments.
Abstract: We have carried out detailed statistical analyses of integral membrane proteins of the helix-bundle class from eubacterial, archaean, and eukaryotic organisms for which genome-wide sequence data are available. Twenty to 30% of all ORFs are predicted to encode membrane proteins, with the larger genomes containing a higher fraction than the smaller ones. Although there is a general tendency that proteins with a smaller number of transmembrane segments are more prevalent than those with many, uni-cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegans and Homo sapiens have a slight preference for proteins with seven transmembrane segments. In all organisms, there is a tendency that membrane proteins either have many transmembrane segments with short connecting loops or few transmembrane segments with large extra-membraneous domains. Membrane proteins from all organisms studied, except possibly the archaeon Methanococcus jannaschii, follow the so-called "positive-inside" rule; i.e., they tend to have a higher frequency of positively charged residues in cytoplasmic than in extra-cytoplasmic segments.

1,519 citations

Journal ArticleDOI
TL;DR: An attempt is made to correlate metabolic stability of proteins with features of their primary sequence where weight values of instability for a protein of known sequence could thus be used as an index for predicting its stability characteristics.
Abstract: Statistical analysis of 12 unstable and 32 stable proteins revealed that there are certain dipeptides, the occurrence of which is significantly different in the unstable proteins compared with those in the stable ones. Based on the impact of these dipeptides on the unstable proteins over the stable ones, a weight value of instability is assigned to each of the dipeptides. For a given protein the summation of these weight values normalized to the length of its sequence helps to distinguish between unstable and stable proteins. Results suggest that the in vivo instability of proteins is possibly determined by the order of certain amino acids in its sequence. An attempt is made to correlate metabolic stability of proteins with features of their primary sequence where weight values of instability for a protein of known sequence could thus be used as an index for predicting its stability characteristics.

1,038 citations

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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20211
20203
20182
20165
20151
20143