Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Resource allocation and scheduling of multiple composite web services in cloud computing using cooperative coevolution genetic algorithm

In cloud computing, resource allocation and scheduling of multiple composite web services is an important and challenging problem. This is especially so in a hybrid cloud where there may be some low-cost resources available from private clouds and some high-cost resources from public clouds. Meeting this challenge involves two classical computational problems: one is assigning resources to each of the tasks in the composite web services; the other is scheduling the allocated resources when each resource may be used by multiple tasks at different points of time. In addition, Quality-of-Service (QoS) issues, such as execution time and running costs, must be considered in the resource allocation and scheduling problem. Here we present a Cooperative Coevolutionary Genetic Algorithm (CCGA) to solve the deadline-constrained resource allocation and scheduling problem for multiple composite web services. Experimental results show that our CCGA is both efficient and scalable.

Characterizing the signal pattern of a four-cylinder diesel engine using acoustic emission and vibration analysis

Condition monitoring of diesel engines can prevent unpredicted engine failures and the associated consequence. This paper presents an experimental study of the signal characteristics of a 4-cylinder diesel engine under various loading conditions. Acoustic emission, vibration and in-cylinder pressure signals were employed to study the effectiveness of these techniques for condition monitoring and identifying symptoms of incipient failures. An event driven synchronous averaging technique was employed to average the quasi-periodic diesel engine signal in the time domain to eliminate or minimize the effect of engine speed and amplitude variations on the analysis of condition monitoring signal. It was shown that acoustic emission (AE) is a better technique than vibration method for condition monitor of diesel engines due to its ability to produce high quality signals (i.e., excellent signal to noise ratio) in a noisy diesel engine environment. It was found that the peak amplitude of AE RMS signals correlating to the impact-like combustion related events decreases in general due to a more stable mechanical process of the engine as the loading increases. A small shift in the exhaust valve closing time was observed as the engine load increases which indicates a prolong combustion process in the cylinder (to produce more power). On the contrary, peak amplitudes of the AE RMS attributing to fuel injection increase as the loading increases. This can be explained by the increase fuel friction caused by the increase volume flow rate during the injection. Multiple AE pulses during the combustion process were identified in the study, which were generated by the piston rocking motion and the interaction between the piston and the cylinder wall. The piston rocking motion is caused by the non-uniform pressure distribution acting on the piston head as a result of the non-linear combustion process of the engine. The rocking motion ceased when the pressure in the cylinder chamber stabilized.