Feature extraction is a key step in membrane protein function prediction, and multifeature fusion not only enhances their complementary but also improves the model prediction performance. Siva et al.4used pseudoamino acid composition (PseAAC), amino acid composition (AAC), and physical and chemical p...
In this work, a system based on maximum variance projection (MVP) is proposed to improve the prediction performance of membrane protein types. The feature extraction step is based on a hybridization representation approach by fusing Position-Specific Score Matrix composition. The protein sequences are...
Membrane protein prediction was achieved using the DAVID Bioinformatics Resources (http://david.abcc.ncifcrf.gov/)(42) and the Gene Ontology (GO) annotation (www.geneontology.org) and the TransMembrane Hidden Markov Model (TMHMM, http://www.cbs.dtu.dk/services/TMHMM/). We used PANTHER (...
the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmembrane helices in polytopic proteins. Alternatively, a membrane protein can be monotopic and anchoredviaan...
Test #1: prediction of membrane protein orientation and insertion energy Membrane proteins are thermodynamically stable in the bilayer because of a favorable orientation and insertion energy. Therefore, implicit membrane energy functions must accurately estimate these quantities. First, we evaluated the parti...
Adamian L, Liang J: Prediction of buried helices in multispan alpha helical membrane proteins. RANTS: http://gila.bioengr.uic.edu/lab. Proteins 2006, 63: 1–5. 10.1002/prot.20874 Article CAS PubMed Google Scholar White SH: The progress of membrane protein structure determination. Protein ...
(Supplementary Fig.2b, c). Subsequently, we utilized these selected PPI templates to infer MP-interacting protein candidates by evaluating theirSSIMvalues by searching the complete human proteome database (UniProt12; Supplementary Fig.2d). We compared the PPI prediction accuracies of ourSSIM, six ...
approaches also used logistic regression to represent interactions involving membrane proteins more accurately, their approach is a prediction algorithm designed to identify a particular kind of membrane protein interactions using training sets of interaction data [6,60]. In contrast, we have constructed ...
A powerful and innovative solution for accurate protein structure prediction Life Science Publications Browse the list of peer-reviewed publications using Schrödinger technology in related application areas. Life Science Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membr...
Schematic diagram of the transmembrane protein prediction results. Three different transmembrane prediction applications were applied on the International Protein Index (IPI) Human v.3.39 dataset of 69,731 protein sequences. A consensus approach, where only the proteins predicted as transmembrane by two ...