scholarly journals Improving the accuracy of transmembrane protein topology prediction using evolutionary information

2007 ◽  
Vol 23 (5) ◽  
pp. 538-544 ◽  
Author(s):  
D. T. Jones
Keyword(s):  
Transmembrane Protein ◽  
Evolutionary Information ◽  
Protein Topology ◽  
Transmembrane Protein Topology ◽  
Topology Prediction

scholarly journals Hidden Neural Networks for transmembrane protein topology prediction

2021 ◽  
Author(s):  
Ioannis A. Tamposis ◽  
Dimitra Sarantopoulou ◽  
Margarita C. Theodoropoulou ◽  
Evangelia A. Stasi ◽  
Panagiota I. Kontou ◽  
...  
Keyword(s):  
Neural Networks ◽  
Transmembrane Protein ◽  
Protein Topology ◽  
Transmembrane Protein Topology ◽  
Topology Prediction

THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION

2006 ◽  
Vol 04 (01) ◽  
pp. 109-123 ◽  
Author(s):  
EMILY W. XU ◽  
PAUL KEARNEY ◽  
DANIEL G. BROWN
Keyword(s):  
Prediction Accuracy ◽  
Transmembrane Protein ◽  
Probabilistic Approach ◽  
Protein Structures ◽  
Transmembrane Proteins ◽  
Functional Domains ◽  
Functional Domain ◽  
Protein Topology ◽  
Transmembrane Protein Topology ◽  
Topology Prediction

Transmembrane proteins affect vital cellular functions and pathogenesis, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between the abundance of transmembrane proteins and the scarcity of known membrane protein structures. Their prediction accuracy is still inadequate: TMHMM, the current state-of-the-art method, has less than 52% accuracy in topology prediction on one set of transmembrane proteins of known topology. Based on the observation that there are functional domains that occur preferentially internal or external to the membrane, we have extended the model of TMHMM to incorporate functional domains, using a probabilistic approach originally developed for computational gene finding. Our extension is better than TMHMM in predicting the topology of transmembrane proteins. As prediction of functional domain improves, our system's prediction accuracy will likely improve as well.

scholarly journals MetaTM - a consensus method for transmembrane protein topology prediction

2009 ◽  
Vol 10 (1) ◽  
pp. 314 ◽  
Author(s):  
Martin Klammer ◽  
David N Messina ◽  
Thomas Schmitt ◽  
Erik LL Sonnhammer
Keyword(s):  
Transmembrane Protein ◽  
Consensus Method ◽  
Protein Topology ◽  
Transmembrane Protein Topology ◽  
Topology Prediction
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