Browsing by Author "Charoenkwan, Phasit"

Now showing 1 - 19 of 19

A Study on Genetic Algorithm and Neural Network for Implementing Mini-Games
(2010-01-01)
Charoenkwan, Phasit
;
Fang, Shih-Wei
;
Wong, Sai-Keung
;
資訊工程學系
;
Department of Computer Science
We study on artificial neural network-based controllers which are either trained or evolved by using the supervised or unsupervised learning approach. We employed backpropagation for the supervised method and the genetic algorithm for the unsupervised method. After training the controllers, we applied the controllers to our three newly designed mini-3D games. We performed a comprehensive study on the performance and weaknesses of the controllers. We emerged the controllers as fundamental tools for giving us more understanding about artificial neural network and its effectiveness in imitating players' behaviours.
Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes
(2015-12-09)
Srinivasulu, Yerukala Sathipati
;
Wang, Jyun-Rong
;
Hsu, Kai-Ti
;
Tsai, Ming-Ju
;
Charoenkwan, Phasit
Background: Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been developed for predicting the binding affinity of protein-protein complexes based on structure and functional information. This work aims to predict the binding affinity of heterodimeric protein complexes from sequences only. Results: This work proposes a support vector machine (SVM) based binding affinity classifier, called SVM-BAC, to classify heterodimeric protein complexes based on the prediction of their binding affinity. SVM-BAC identified 14 of 580 sequence descriptors (physicochemical, energetic and conformational properties of the 20 amino acids) to classify 216 heterodimeric protein complexes into low and high binding affinity. SVM-BAC yielded the training accuracy, sensitivity, specificity, AUC and test accuracy of 85.80%, 0.89, 0.83, 0.86 and 83.33%, respectively, better than existing machine learning algorithms. The 14 features and support vector regression were further used to estimate the binding affinities (Pkd) of 200 heterodimeric protein complexes. Prediction performance of a Jackknife test was the correlation coefficient of 0.34 and mean absolute error of 1.4. We further analyze three informative physicochemical properties according to their contribution to prediction performance. Results reveal that the following properties are effective in predicting the binding affinity of heterodimeric protein complexes: apparent partition energy based on buried molar fractions, relations between chemical structure and biological activity in principal component analysis IV, and normalized frequency of beta turn. Conclusions: The proposed sequence-based prediction method SVM-BAC uses an optimal feature selection method to identify 14 informative features to classify and predict binding affinity of heterodimeric protein complexes. The characterization analysis revealed that the average numbers of beta turns and hydrogen bonds at protein-protein interfaces in high binding affinity complexes are more than those in low binding affinity complexes.
Designing predictors of halophilic and non-halophilic proteins using support vector machines
(2013)
Huang, Hui-Ling
;
Charoenkwan, Phasit
;
Srinivasulu, Yerukala Sathipati
;
Lee, Hua-Chin
;
Ho, Shinn-Ying
Finding the molecular features causes the halophilicity in the halostable organisms is helpful to understand the halophilic adaption. In this study, we proposed a prediction method for halophilic proteins by using a machine learning method. The stages of this study are six-fold. First, we establish a non-redundant dataset of the halophilic proteins, collected from NCBI, Uniprotkb and EMBL-EBI databases. The dataset consists of 245 positive and negative proteins with sequence identity < 25%. Second, the protein sequences are represented by three types of feature vector sets which include amino acid composition, dipeptide composition, and physicochemical properties. Third, we propose three classifiers based on support vector machine (SVM) to classify the halophilic proteins and non-halophilic proteins. Fourth, the independent test accuracies of the three efficient classifiers are larger than 83%. Fifth, an inheritable bi-objective combinatory genetic algorithm is utilized to select a set of 11 physicochemical properties (PCPs). Sixth, these abundant amino acids, high different dipeptides (amino acid pair) and 11 informative PCPs can support to analyze the halophilic and non-halophilic proteins.
Discovery of prognostic biomarkers for predicting lung cancer metastasis using microarray and survival data
(2015-02-21)
Huang, Hui-Ling
;
Wu, Yu-Chung
;
Su, Li-Jen
;
Huang, Yun-Ju
;
Charoenkwan, Phasit
Background: Few studies have investigated prognostic biomarkers of distant metastases of lung cancer. One of the central difficulties in identifying biomarkers from microarray data is the availability of only a small number of samples, which results overtraining. Recently obtained evidence reveals that epithelial-mesenchymal transition (EMT) of tumor cells causes metastasis, which is detrimental to patients' survival. Results: This work proposes a novel optimization approach to discovering EMT-related prognostic biomarkers to predict the distant metastasis of lung cancer using both microarray and survival data. This weighted objective function maximizes both the accuracy of prediction of distant metastasis and the area between the disease-free survival curves of the non-distant and distant metastases. Seventy-eight patients with lung cancer and a follow-up time of 120 months are used to identify a set of gene markers and an independent cohort of 26 patients is used to evaluate the identified biomarkers. The medical records of the 78 patients show a significant difference between the disease-free survival times of the 37 non-distant-and the 41 distant-metastasis patients. The experimental results thus obtained are as follows. 1) The use of disease-free survival curves can compensate for the shortcoming of insufficient samples and greatly increase the test accuracy by 11.10%; and 2) the support vector machine with a set of 17 transcripts, such as CCL16 and CDKN2AIP, can yield a leave-one-out cross-validation accuracy of 93.59%, a test accuracy of 76.92%, a large disease-free survival area of 74.81%, and a mean survival prediction error of 3.99 months. The identified putative biomarkers are examined using related studies and signaling pathways to reveal the potential effectiveness of the biomarkers in prospective confirmatory studies. Conclusions: The proposed new optimization approach to identifying prognostic biomarkers by combining multiple sources of data (microarray and survival) can facilitate the accurate selection of biomarkers that are most relevant to the disease while solving the problem of insufficient samples.
HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening
(2013-10-22)
Charoenkwan, Phasit
;
Hwang, Eric
;
Cutler, Robert W.
;
Lee, Hua-Chin
;
Ko, Li-Wei
Background: High-content screening (HCS) has become a powerful tool for drug discovery. However, the discovery of drugs targeting neurons is still hampered by the inability to accurately identify and quantify the phenotypic changes of multiple neurons in a single image (named multi-neuron image) of a high-content screen. Therefore, it is desirable to develop an automated image analysis method for analyzing multi-neuron images. Results: We propose an automated analysis method with novel descriptors of neuromorphology features for analyzing HCS-based multi-neuron images, called HCS-neurons. To observe multiple phenotypic changes of neurons, we propose two kinds of descriptors which are neuron feature descriptor (NFD) of 13 neuromorphology features, e. g., neurite length, and generic feature descriptors (GFDs), e. g., Haralick texture. HCS-neurons can 1) automatically extract all quantitative phenotype features in both NFD and GFDs, 2) identify statistically significant phenotypic changes upon drug treatments using ANOVA and regression analysis, and 3) generate an accurate classifier to group neurons treated by different drug concentrations using support vector machine and an intelligent feature selection method. To evaluate HCS-neurons, we treated P19 neurons with nocodazole (a microtubule depolymerizing drug which has been shown to impair neurite development) at six concentrations ranging from 0 to 1000 ng/mL. The experimental results show that all the 13 features of NFD have statistically significant difference with respect to changes in various levels of nocodazole drug concentrations (NDC) and the phenotypic changes of neurites were consistent to the known effect of nocodazole in promoting neurite retraction. Three identified features, total neurite length, average neurite length, and average neurite area were able to achieve an independent test accuracy of 90.28% for the six-dosage classification problem. This NFD module and neuron image datasets are provided as a freely downloadable MatLab project at http://iclab.life.nctu.edu.tw/HCS-Neurons. Conclusions: Few automatic methods focus on analyzing multi-neuron images collected from HCS used in drug discovery. We provided an automatic HCS-based method for generating accurate classifiers to classify neurons based on their phenotypic changes upon drug treatments. The proposed HCS-neurons method is helpful in identifying and classifying chemical or biological molecules that alter the morphology of a group of neurons in HCS.
NeurphologyJ: An automatic neuronal morphology quantification method and its application in pharmacological discovery
(2011-06-08)
Ho, Shinn-Ying
;
Chao, Chih-Yuan
;
Huang, Hui-Ling
;
Chiu, Tzai-Wen
;
Charoenkwan, Phasit
Background: Automatic quantification of neuronal morphology from images of fluorescence microscopy plays an increasingly important role in high-content screenings. However, there exist very few freeware tools and methods which provide automatic neuronal morphology quantification for pharmacological discovery. Results: This study proposes an effective quantification method, called NeurphologyJ, capable of automatically quantifying neuronal morphologies such as soma number and size, neurite length, and neurite branching complexity (which is highly related to the numbers of attachment points and ending points). NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image processing and analysis platform. The high performance of NeurphologyJ arises mainly from an elegant image enhancement method. Consequently, some morphology operations of image processing can be efficiently applied. We evaluated NeurphologyJ by comparing it with both the computer-aided manual tracing method NeuronJ and an existing ImageJ-based plugin method NeuriteTracer. Our results reveal that NeurphologyJ is comparable to NeuronJ, that the coefficient correlation between the estimated neurite lengths is as high as 0.992. NeurphologyJ can accurately measure neurite length, soma number, neurite attachment points, and neurite ending points from a single image. Furthermore, the quantification result of nocodazole perturbation is consistent with its known inhibitory effect on neurite outgrowth. We were also able to calculate the IC50 of nocodazole using NeurphologyJ. This reveals that NeurphologyJ is effective enough to be utilized in applications of pharmacological discoveries. Conclusions: This study proposes an automatic and fast neuronal quantification method NeurphologyJ. The ImageJ plugin with supports of batch processing is easily customized for dealing with high-content screening applications. The source codes of NeurphologyJ (interactive and high-throughput versions) and the images used for testing are freely available (see Availability).
POC: Paphiopedilum Orchid Classifier
(2015)
Arwatchananukul, Sujitra
;
Charoenkwan, Phasit
;
Xu, Dan
;
生物資訊及系統生物研究所
;
Institude of Bioinformatics and Systems Biology
Paphiopedilum Orchid Flowers (POF) are colorful wildflowers and also endangered plants since they bloom only one time per year. There are many species with a similar appearance, which makes it difficult and laborious to classify. Thus, we propose a novel Paphiopedilum Orchid Classifier (POC) based on Neural Network, utilizing the Color and Segmentation-based Fractal Texture Analysis (SFTA) features. In the classification of 11 POF species, POC achieved 97.64% of 10-fold cross validation accuracy. Besides, we also propose a new POF dataset consisting of 100 samples for each species and illustrated the prediction performance of several renowned classifiers such as Naive Bayes, K-nearest and Decision Tree. According to research result, we hope that POC can assists botanists to classify POF for further breed selection and adaptation.
Predicting Neuroinflammation in Morphine Tolerance for Tolerance Therapy from Immunostaining Images of Rat Spinal Cord
(2015-10-05)
Lin, Shinn-Long
;
Chang, Fang-Lin
;
Ho, Shinn-Ying
;
Charoenkwan, Phasit
;
Wang, Kuan-Wei
Long-term morphine treatment leads to tolerance which attenuates analgesic effect and hampers clinical utilization. Recent studies have sought to reveal the mechanism of opioid receptors and neuroinflammation by observing morphological changes of cells in the rat spinal cord. This work proposes a high-content screening (HCS) based computational method, HCS-Morph, for predicting neuroinflammation in morphine tolerance to facilitate the development of tolerance therapy using immunostaining images for astrocytes, microglia, and neurons in the spinal cord. HCS-Morph first extracts numerous HCS-based features of cellular phenotypes. Next, an inheritable bi-objective genetic algorithm is used to identify a minimal set of features by maximizing the prediction accuracy of neuroinflammation. Finally, a mathematic model using a support vector machine with the identified features is established to predict drug-treated images to assess the effects of tolerance therapy. The dataset consists of 15 saline controls (1 mu l/h), 15 morphine-tolerant rats (15 mu g/h), and 10 rats receiving a co-infusion of morphine (15 mu g/h) and gabapentin (15 mu g/h, Sigma). The three individual models of astrocytes, microglia, and neurons for predicting neuroinflammation yielded respective Jackknife test accuracies of 96.67%, 90.00%, and 86.67% on the 30 rats, and respective independent test accuracies of 100%, 90%, and 60% on the 10 co-infused rats. The experimental results suggest that neuroinflammation activity expresses more predominantly in astrocytes and microglia than in neuron cells. The set of features for predicting neuroinflammation from images of astrocytes comprises mean cell intensity, total cell area, and second-order geometric moment (relating to cell distribution), relevant to cell communication, cell extension, and cell migration, respectively. The present investigation provides the first evidence for the role of gabapentin in the attenuation of morphine tolerance from phenotypic changes of astrocytes and microglia. Based on neuroinflammation prediction, the proposed computer-aided image diagnosis system can greatly facilitate the development of tolerance therapy with anti-inflammatory drugs.
Predicting Protein Crystallization Using a Simple Scoring Card Method
(2013)
Shoombuatong, Watshara
;
Charoenkwan, Phasit
;
Huang, Hui-Ling
;
Lee, Hua-Chin
;
Chaijaruwanich, Jeerayut
Many computational methods have been developed to predict protein crystallization. Most methods use amino acid and dipeptide compositions as part of the informative features. To advance the prediction accuracy, the support vector machine (SVM) based classifiers and ensemble approaches were effective and commonly-used techniques. However, these techniques suffer from the low interpretation ability of insight into crystallization. In this study, we utilize a newly-developed scoring card method (SCM) with a dipeptide composition feature to predict protein crystallization. This SCM classifier obtains prediction results 74%, 0.55 and 0.83 for accuracy, sensitivity and specificity, respectively, which is comparable to the SVM classifier using the same benchmarks. The experimental results show that the SCM classifier has advantages of simplicity, high interpretability, and high accuracy in predicting protein crystallization, compared with existing SVM-based ensemble classifiers.
Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition
(2012-12-13)
Huang, Hui-Ling
;
Charoenkwan, Phasit
;
Kao, Te-Fen
;
Lee, Hua-Chin
;
Chang, Fang-Lin
Background: Existing methods for predicting protein solubility on overexpression in Escherichia coli advance performance by using ensemble classifiers such as two-stage support vector machine (SVM) based classifiers and a number of feature types such as physicochemical properties, amino acid and dipeptide composition, accompanied with feature selection. It is desirable to develop a simple and easily interpretable method for predicting protein solubility, compared to existing complex SVM-based methods. Results: This study proposes a novel scoring card method (SCM) by using dipeptide composition only to estimate solubility scores of sequences for predicting protein solubility. SCM calculates the propensities of 400 individual dipeptides to be soluble using statistic discrimination between soluble and insoluble proteins of a training data set. Consequently, the propensity scores of all dipeptides are further optimized using an intelligent genetic algorithm. The solubility score of a sequence is determined by the weighted sum of all propensity scores and dipeptide composition. To evaluate SCM by performance comparisons, four data sets with different sizes and variation degrees of experimental conditions were used. The results show that the simple method SCM with interpretable propensities of dipeptides has promising performance, compared with existing SVM-based ensemble methods with a number of feature types. Furthermore, the propensities of dipeptides and solubility scores of sequences can provide insights to protein solubility. For example, the analysis of dipeptide scores shows high propensity of a-helix structure and thermophilic proteins to be soluble. Conclusions: The propensities of individual dipeptides to be soluble are varied for proteins under altered experimental conditions. For accurately predicting protein solubility using SCM, it is better to customize the score card of dipeptide propensities by using a training data set under the same specified experimental conditions. The proposed method SCM with solubility scores and dipeptide propensities can be easily applied to the protein function prediction problems that dipeptide composition features play an important role. Availability: The used datasets, source codes of SCM, and supplementary files are available at http://iclab.life.nctu.edu.tw/SCM/.
Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition
(2012-12-13)
Huang, Hui-Ling
;
Charoenkwan, Phasit
;
Kao, Te-Fen
;
Lee, Hua-Chin
;
Chang, Fang-Lin
Background: Existing methods for predicting protein solubility on overexpression in Escherichia coli advance performance by using ensemble classifiers such as two-stage support vector machine (SVM) based classifiers and a number of feature types such as physicochemical properties, amino acid and dipeptide composition, accompanied with feature selection. It is desirable to develop a simple and easily interpretable method for predicting protein solubility, compared to existing complex SVM-based methods. Results: This study proposes a novel scoring card method (SCM) by using dipeptide composition only to estimate solubility scores of sequences for predicting protein solubility. SCM calculates the propensities of 400 individual dipeptides to be soluble using statistic discrimination between soluble and insoluble proteins of a training data set. Consequently, the propensity scores of all dipeptides are further optimized using an intelligent genetic algorithm. The solubility score of a sequence is determined by the weighted sum of all propensity scores and dipeptide composition. To evaluate SCM by performance comparisons, four data sets with different sizes and variation degrees of experimental conditions were used. The results show that the simple method SCM with interpretable propensities of dipeptides has promising performance, compared with existing SVM-based ensemble methods with a number of feature types. Furthermore, the propensities of dipeptides and solubility scores of sequences can provide insights to protein solubility. For example, the analysis of dipeptide scores shows high propensity of a-helix structure and thermophilic proteins to be soluble. Conclusions: The propensities of individual dipeptides to be soluble are varied for proteins under altered experimental conditions. For accurately predicting protein solubility using SCM, it is better to customize the score card of dipeptide propensities by using a training data set under the same specified experimental conditions. The proposed method SCM with solubility scores and dipeptide propensities can be easily applied to the protein function prediction problems that dipeptide composition features play an important role. Availability: The used datasets, source codes of SCM, and supplementary files are available at http://iclab.life.nctu.edu.tw/SCM/.
Prediction of Mouse Senescence from HE-Stain Liver Images Using an Ensemble SVM Classifier
(2013)
Huang, Hui-Ling
;
Hsu, Ming-Hsin
;
Lee, Hua-Chin
;
Charoenkwan, Phasit
;
Ho, Shinn-Jang
Study of cellular senescence from images in molecular level plays an important role in understanding the molecular basis of ageing. It is desirable to know the morphological variation between young and senescent cells. This study proposes an ensemble support vector machine (SVM) based classifier with a novel set of image features to predict mouse senescence from HE-stain liver images categorized into four classes. For the across-subject prediction that all images of the same mouse are divided into training and test images, the test accuracy is as high as 97.01% by selecting an optimal set of informative image features using an intelligent genetic algorithm. For the leave-one-subject-out prediction that the test mouse is not involved in the training images of 20 mice, we identified eight informative feature sets and established eight SVM classifiers with a single feature set. The best accuracy of using an SVM classifier is 71.73% and the ensemble classifier consisting of these eight SVM classifiers can advance performance with accuracy of 80.95%. The best two feature sets are the gray level correlation matrix for describing texture and Haralick texture set, which are good morphological features in studying cellular senescence.
Recognition of handwritten Lanna Dhamma characters using a set of optimally designed moment features
(2017-12-01)
Inkeaw, Papangkorn
;
Charoenkwan, Phasit
;
Huang, Hui-Ling
;
Marukatat, Sanparith
;
Ho, Shinn-Ying
Lanna Dhamma alphabet was used mainly for religious communication in the ancient Lanna Kingdom of Thailand. The old manuscripts using this alphabet are gradually decayed. It is desirable to preserve these valuable manuscripts in machine-encoded text files. Existing works used optical character recognition (OCR) methods based on wavelet transform for recognition of handwritten Lanna Dhamma characters. However, the test accuracy of writer-independent recognition is not satisfactory. This work proposes an OCR method, called LDIMS, for recognition of handwritten Lanna Dhamma characters using a set of optimally designed moment features. The LDIMS using an optimization approach to feature selection consists of three main phases: (1) determination of moment orders for each of eight effective moment descriptors, (2) the best combination of selected moment descriptors and (3) the optimized selection of moment features using an inheritable bi-objective genetic algorithm. The LDIMS has three individual feature sets for the recognition of handwritten Lanna Dhamma characters in upper, middle and lower levels. The character images gleaned from previous work were used as a training dataset. A new character image dataset from different writers was established for evaluating ability of writer-independent recognition. The experimental results show that the LDIMS using four moment descriptors, Meixner, Charlier, Tchebichef and Hahn, has test accuracies of 86.60, 74.38 and 85.82% for the characters in upper, middle and lower levels, respectively. The LDIMS with a mean accuracy of 82.27% performed well in recognizing the handwritten Lanna Dhamma characters from new writers, compared to existing methods using generic descriptors in terms of both accuracy and feature number used. Experimental results show that the generalized OCR method, LDIMS, is also effective for character recognition of digit and English alphabets, compared to existing methods.
Recognition-based character segmentation for multi-level writing style
(2018-06-01)
Inkeaw, Papangkorn
;
Bootkrajang, Jakramate
;
Charoenkwan, Phasit
;
Marukatat, Sanparith
;
Ho, Shinn-Ying
Character segmentation is an important task in optical character recognition (OCR). The quality of any OCR system is highly dependent on character segmentation algorithm. Despite the availability of various character segmentation methods proposed to date, existing methods cannot satisfyingly segment characters belonging to some complex writing styles such as the Lanna Dhamma characters. In this paper, a new character segmentation method named graph partitioning-based character segmentation is proposed to address the problem. The proposed method can deal with multi-level writing style as well as touching and broken characters. It is considered as a generalization of existing approaches to multi-level writing style. The proposed method consists of three phases. In the first phase, a newly devised over-segmentation technique based on morphological skeleton is used to obtain redundant fragments of a word image. The fragments are then used to form a segmentation hypotheses graph. In the last phase, the hypotheses graph is partitioned into subgraphs each corresponding to a segmented character using the partitioning algorithm developed specifically for character segmentation purpose. Experimental results based on handwritten Lanna Dhamma characters datasets showed that the proposed method achieved high correct segmentation rate and outperformed existing methods for the Lanna Dhamma alphabet.
Rule-Based Page Segmentation for Palm Leaf Manuscript on Color Image
(2016)
Inkeaw, Papangkorn
;
Bootkrajang, Jakramate
;
Charoenkwan, Phasit
;
Marukatat, Sanparith
;
Ho, Shinn-Ying
Palm leaf manuscripts are important source of history and ancient wisdom. Large number of manuscripts have been already digitized in the form of folio images. To extract useful information, an optical character recognition (OCR) is often considered to be the first step towards text mining. Unfortunately, folio images contain multiple unsegmented palm leaf images, making it difficult to manage in OCR process. This motivates us to propose a new page segmentation method for palm leaf manuscripts. This method consists of two main steps, first of which is the detection of objects in folio images using Connected Component Labeling method in a transformed L*a*b* color space. The second step is rule- based selection of objects as either palm leaf or not palm leaf. The experiments performed on 20 publicly available palm leaf manuscripts composed of 384 folio images demonstrated that the proposed method effectively segmented folio images into separate palm leaf images, with 99.86% precision and 96.67% recall scores.
SCMCRYS: Predicting Protein Crystallization Using an Ensemble Scoring Card Method with Estimating Propensity Scores of P-Collocated Amino Acid Pairs
(2013-09-03)
Charoenkwan, Phasit
;
Shoombuatong, Watshara
;
Lee, Hua-Chin
;
Chaijaruwanich, Jeerayut
;
Huang, Hui-Ling
Existing methods for predicting protein crystallization obtain high accuracy using various types of complemented features and complex ensemble classifiers, such as support vector machine (SVM) and Random Forest classifiers. It is desirable to develop a simple and easily interpretable prediction method with informative sequence features to provide insights into protein crystallization. This study proposes an ensemble method, SCMCRYS, to predict protein crystallization, for which each classifier is built by using a scoring card method (SCM) with estimating propensity scores of p-collocated amino acid (AA) pairs (p = 0 for a dipeptide). The SCM classifier determines the crystallization of a sequence according to a weighted-sum score. The weights are the composition of the p-collocated AA pairs, and the propensity scores of these AA pairs are estimated using a statistic with optimization approach. SCMCRYS predicts the crystallization using a simple voting method from a number of SCM classifiers. The experimental results show that the single SCM classifier utilizing dipeptide composition with accuracy of 73.90% is comparable to the best previously-developed SVM-based classifier, SVM_POLY (74.6%), and our proposed SVM-based classifier utilizing the same dipeptide composition (77.55%). The SCMCRYS method with accuracy of 76.1% is comparable to the state-of-the-art ensemble methods PPCpred (76.8%) and RFCRYS (80.0%), which used the SVM and Random Forest classifiers, respectively. This study also investigates mutagenesis analysis based on SCM and the result reveals the hypothesis that the mutagenesis of surface residues Ala and Cys has large and small probabilities of enhancing protein crystallizability considering the estimated scores of crystallizability and solubility, melting point, molecular weight and conformational entropy of amino acids in a generalized condition. The propensity scores of amino acids and dipeptides for estimating the protein crystallizability can aid biologists in designing mutation of surface residues to enhance protein crystallizability. The source code of SCMCRYS is available at http://iclab.life.nctu.edu.tw/SCMCRYS/.
SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides
(2014-12-08)
Liou, Yi-Fan
;
Charoenkwan, Phasit
;
Srinivasulu, Yerukala Sathipati
;
Vasylenko, Tamara
;
Lai, Shih-Chung
Background: Heme binding proteins (HBPs) are metalloproteins that contain a heme ligand (an iron-porphyrin complex) as the prosthetic group. Several computational methods have been proposed to predict heme binding residues and thereby to understand the interactions between heme and its host proteins. However, few in silico methods for identifying HBPs have been proposed. Results: This work proposes a scoring card method (SCM) based method (named SCMHBP) for predicting and analyzing HBPs from sequences. A balanced dataset of 747 HBPs (selected using a Gene Ontology term GO: 0020037) and 747 non-HBPs (selected from 91,414 putative non-HBPs) with an identity of 25% was firstly established. Consequently, a set of scores that quantified the propensity of amino acids and dipeptides to be HBPs is estimated using SCM to maximize the predictive accuracy of SCMHBP. Finally, the informative physicochemical properties of 20 amino acids are identified by utilizing the estimated propensity scores to be used to categorize HBPs. The training and mean test accuracies of SCMHBP applied to three independent test datasets are 85.90% and 71.57%, respectively. SCMHBP performs well relative to comparison with such methods as support vector machine (SVM), decision tree J48, and Bayes classifiers. The putative non-HBPs with high sequence propensity scores are potential HBPs, which can be further validated by experimental confirmation. The propensity scores of individual amino acids and dipeptides are examined to elucidate the interactions between heme and its host proteins. The following characteristics of HBPs are derived from the propensity scores: 1) aromatic side chains are important to the effectiveness of specific HBP functions; 2) a hydrophobic environment is important in the interaction between heme and binding sites; and 3) the whole HBP has low flexibility whereas the heme binding residues are relatively flexible. Conclusions: SCMHBP yields knowledge that improves our understanding of HBPs rather than merely improves the prediction accuracy in predicting HBPs.
SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides
(2015-12-09)
Liou, Yi-Fan
;
Vasylenko, Tamara
;
Yeh, Chia-Lun
;
Lin, Wei-Chun
;
Chiu, Shih-Hsiang
Background: Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanisms involved remain important challenges for the advancement of structural and functional genomics. However, the transporter characters are mainly acquired from MTP crystal structures which are hard to crystalize. Therefore, it is desirable to develop bioinformatics tools for the effective large-scale analysis of available sequences to identify novel transporters and characterize such transporters. Results: This work proposes a novel method (SCMMTP) based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset containing 900 MTPs and 660 non-MTPs which are separated into a training dataset consisting 1,380 proteins and an independent dataset consisting 180 proteins. The SCMMTP produced estimating propensity scores for amino acids and dipeptides as MTPs. The SCMMTP training and test accuracy levels respectively reached 83.81% and 76.11%. The test accuracy of support vector machine (SVM) using a complicated classification method with a low possibility for biological interpretation and position-specific substitution matrix (PSSM) as a protein feature is 80.56%, thus SCMMTP is comparable to SVM-PSSM. To identify MTPs, SCMMTP is applied to three datasets including: 1) human transmembrane proteins, 2) a photosynthetic protein dataset, and 3) a human protein database. MTPs showing a-helix rich structure is agreed with previous studies. The MTPs used residues with low hydration energy. It is hypothesized that, after filtering substrates, the hydrated water molecules need to be released from the pore regions. Conclusions: SCMMTP yields estimating propensity scores for amino acids and dipeptides as MTPs, which can be used to identify novel MTPs and characterize transport mechanisms for use in further experiments. Availability: http://iclab.life.nctu.edu.tw/iclab_webtools/SCMMTP/
SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method
(2015-01-21)
Vasylenko, Tamara
;
Liou, Yi-Fan
;
Chen, Hong-An
;
Charoenkwan, Phasit
;
Huang, Hui-Ling
Background: Photosynthetic proteins (PSPs) greatly differ in their structure and function as they are involved in numerous subprocesses that take place inside an organelle called a chloroplast. Few studies predict PSPs from sequences due to their high variety of sequences and structues. This work aims to predict and characterize PSPs by establishing the datasets of PSP and non-PSP sequences and developing prediction methods. Results: A novel bioinformatics method of predicting and characterizing PSPs based on scoring card method (SCMPSP) was used. First, a dataset consisting of 649 PSPs was established by using a Gene Ontology term GO: 0015979 and 649 non-PSPs from the SwissProt database with sequence identity <= 25%.- Several prediction methods are presented based on support vector machine (SVM), decision tree J48, Bayes, BLAST, and SCM. The SVM method using dipeptide features-performed well and yielded - a test accuracy of 72.31%. The SCMPSP method uses the estimated propensity scores of 400 dipeptides - as PSPs and has a test accuracy of 71.54%, which is comparable to that of the SVM method. The derived propensity scores of 20 amino acids were further used to identify informative physicochemical properties for characterizing PSPs. The analytical results reveal the following four characteristics of PSPs: 1) PSPs favour hydrophobic side chain amino acids; 2) PSPs are composed of the amino acids prone to form helices in membrane environments; 3) PSPs have low interaction with water; and 4) PSPs prefer to be composed of the amino acids of electron-reactive side chains. Conclusions: The SCMPSP method not only estimates the propensity of a sequence to be PSPs, it also discovers characteristics that further improve understanding of PSPs. The SCMPSP source code and the datasets used in this study are available at http://iclab.life.nctu.edu.tw/SCMPSP/.