* Background In the search for therapeutic peptides for disease treatments, many efforts have been made to identify various functional peptides from large numbers of peptide sequence databases. In this paper, we propose an effective computational model that uses deep learning and word2vec to predict therapeutic peptides (PTPD). * Results Representation vectors of all k -mers were obtained through word2vec based on k -mer co-existence information. The original peptide sequences were then divided into k -mers using the windowing method. The peptide sequences were mapped to the input layer by the embedding vector obtained by word2vec. Three types of filters in the convolutional layers, as well as dropout and max-pooling operations, were applied to construct feature maps. These feature maps were concatenated into a fully connected dense layer, and rectified linear units (ReLU) and dropout operations were included to avoid over-fitting of PTPD. The classification probabilities were generated by a sigmoid function. PTPD was then validated using two datasets: an independent anticancer peptide dataset and a virulent protein dataset, on which it achieved accuracies of 96% and 94%, respectively. * Conclusions PTPD identified novel therapeutic peptides efficiently, and it is suitable for application as a useful tool in therapeutic peptide design.

The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew’s Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions.

Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution), bi-profile Bayes, PseAAC (pseudo-amino acid composition) and PSSM (position-specific scoring matrix). When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew’s correlation coefficient (MCC) of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.

BackgroundAptamer-protein interacting pairs play a variety of physiological functions and therapeutic potentials in organisms. Rapidly and effectively predicting aptamer-protein interacting pairs is significant to design aptamers binding to certain interested proteins, which will give insight into understanding mechanisms of aptamer-protein interacting pairs and developing aptamer-based therapies.ResultsIn this study, an ensemble method is presented to predict aptamer-protein interacting pairs with hybrid features. The features for aptamers are extracted from Pseudo K-tuple Nucleotide Composition (PseKNC) while the features for proteins incorporate Discrete Cosine Transformation (DCT), disorder information, and bi-gram Position Specific Scoring Matrix (PSSM). We investigate predictive capabilities of various feature spaces. The proposed ensemble method obtains the best performance with Youden’s Index of 0.380, using the hybrid feature space of PseKNC, DCT, bi-gram PSSM, and disorder information by 10-fold cross validation. The Relief-Incremental Feature Selection (IFS) method is adopted to obtain the optimal feature set. Based on the optimal feature set, the proposed method achieves a balanced performance with a sensitivity of 0.753 and a specificity of 0.725 on the training dataset, which indicates that this method can solve the imbalanced data problem effectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous study with a sensitivity of 0.738 and a Youden’s Index of 0.451.ConclusionsThese results suggest that the proposed method can be a potential candidate for aptamer-protein interacting pair prediction, which may contribute to finding novel aptamer-protein interacting pairs and understanding the relationship between aptamers and proteins.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1087-5) contains supplementary material, which is available to authorized users.

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Underwater navigation that relies solely on dead reckoning (DR) suffers from unbounded position error growth. A common approach for alleviating the problem is to have the underwater vehicle surface occasionally for a Global Positioning System (GPS) fix, at the risk of jeopardizing the vehicle's safety and consuming precious mission time. Other alternatives include deploying a long-baseline (LBL) acoustic positioning system in the mission area; this involves substantial deployment effort. The idea of having active mobile beacons as navigational aids has recently gained interest. We explore the use of a single-beacon vehicle for range-only localization to support other autonomous underwater vehicles (AUVs). Specifically, we focus on cooperative path-planning algorithms for the beacon vehicle using dynamic programming and Markov decision process formulations. These formulations take into account and minimize the positioning errors being accumulated by the supported AUV. This approach avoids the use of LBL acoustic positioning systems as well as allows the supported AUV to remain submerged for a longer period of time with small position error. Simulation results and field trials data demonstrate that the beacon vehicle is able to help keep the position error of the supported AUV small via acoustic range measurements.

In this paper, we propose a new framework for solving state estimation problems with an additional sparsitypromoting L1-regularizer term. We first formulate such problems as minimization of the sum of linear or nonlinear quadratic error terms and an extra regularizer, and then present novel algorithms which solve the linear and nonlinear cases. The methods are based on a combination of the iterated extended Kalman smoother and variable splitting techniques such as alternating direction method of multipliers (ADMM). We present a general algorithmic framework for variable splitting methods, where the iterative steps involving minimization of the nonlinear quadratic terms can be computed efficiently by iterated smoothing. Due to the use of state estimation algorithms, the proposed framework has a low per-iteration time complexity, which makes it suitable for solving a large-scale or high-dimensional state estimation problem. We also provide convergence results for the proposed algorithms. The experiments show the promising performance and speed-ups provided by the methods.

The paper addresses the image fusion problem, where multiple images captured with different focus distances are to be combined into a higher quality all-in-focus image. Most current approaches for image fusion strongly rely on the unrealistic noise-free assumption used during the image acquisition, and then yield limited robustness in fusion processing. In our approach, we formulate the multi-focus image fusion problem in terms of an analysis sparse model, and simultaneously perform the restoration and fusion of multi-focus images. Based on this model, we propose an analysis operator learning, and define a novel fusion function to generate an all-in-focus image. Experimental evaluations confirm the effectiveness of the proposed fusion approach both visually and quantitatively, and show that our approach outperforms state-of-the-art fusion methods.Comment: 12 pages, 4 figures, 1 table, Submitted to IEEE Signal Processing Letters on December 201