Aarti Garg

University of Padua, Padova, Veneto, Italy

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Publications (19)40.52 Total impact

  • Article: Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information.
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    ABSTRACT: The study of reliable automatic system for predicting bacterial virulent proteins has several important applications for finding novel drug/vaccine and for understanding virulence mechanisms in pathogens. In this work we study several feature extraction approaches for representing proteins and propose a novel bacterial virulent protein prediction method based on an ensemble of classifiers where the features are extracted directly from the amino acid sequence and from the evolutionary information of a given protein. In particular, several ensembles are evaluated and compared, obtained combining six feature extraction methods and several classification approaches based on two general purpose classifiers (i.e. support vector machine and a variant of input decimated ensemble) and their random subspace version. An extensive evaluation performed according to a blind testing protocol, where the parameters of the system are optimized using the training set and the system is validated in three different independent datasets, allows selecting the most performing system and demonstrates the validity of the proposed method. Based on the results obtained using the blind testing protocol, it is interesting to note that, even if in each independent dataset the most performing stand-alone method is not always the same, the fusion among different methods permits to obtain a good performance stability in all the tested independent datasets.
    IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 08/2011; · 2.25 Impact Factor
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    Article: KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials.
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    ABSTRACT: Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general. This paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value (Ki) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R/q2 of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R/q2 values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values (q2/r2) in the range of 0.78-0.83/0.93-0.95. Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq, which allows the prediction of Ki value of a new ligand molecule against DHDPS.
    BMC Bioinformatics 03/2010; 11:125. · 2.75 Impact Factor
  • Article: K
    BMC Bioinformatics. 01/2010; 11:125.
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    Article: Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of
    BMC Bioinformatics. 01/2010; 11:53.
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    Article: Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis
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    ABSTRACT: Abstract Background An explosive global spreading of multidrug resistant Mycobacterium tuberculosis ( Mtb ) is a catastrophe, which demands an urgent need to design or develop novel/potent antitubercular agents. The Lysine/DAP biosynthetic pathway is a promising target due its specific role in cell wall and amino acid biosynthesis. Here, we report identification of potential antitubercular candidates targeting Mtb dihydrodipicolinate synthase (DHDPS) enzyme of the pathway using virtual screening protocols. Results In the present study, we generated three sets of drug-like molecules in order to screen potential inhibitors against Mtb drug target DHDPS. The first set of compounds was a combinatorial library, which comprised analogues of pyruvate (substrate of DHDPS). The second set of compounds consisted of pyruvate-like molecules i.e. structurally similar to pyruvate, obtained using 3D flexible similarity search against NCI and PubChem database. The third set constituted 3847 anti-infective molecules obtained from PubChem. These compounds were subjected to Lipinski's rule of drug-like five filters. Finally, three sets of drug-like compounds i.e. 4088 pyruvate analogues, 2640 pyruvate-like molecules and 1750 anti-infective molecules were docked at the active site of Mtb DHDPS (PDB code: 1XXX used in the molecular docking calculations) to select inhibitors establishing favorable interactions. Conclusion The above-mentioned virtual screening procedures helped in the identification of several potent candidates that possess inhibitory activity against Mtb DHDPS. Therefore, these novel scaffolds/candidates which could have the potential to inhibit Mtb DHDPS enzyme would represent promising starting points as lead compounds and certainly aid the experimental designing of antituberculars in lesser time.
    BMC Bioinformatics. 01/2010;
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    Article: K i DoQ: using docking based energy scores to develop ligand based model for predicting antibacterials
    [show abstract] [hide abstract]
    ABSTRACT: Abstract Background Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general. Results This paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value ( K <sub>i</sub>) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R / q <sup>2 </sup>of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R / q <sup>2 </sup>values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values ( q <sup>2</sup>/ r <sup>2</sup>) in the range of 0.78-0.83/0.93-0.95. Conclusions Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "K i DoQ" has been developed http://crdd.osdd.net/raghava/kidoq , which allows the prediction of K <sub>i </sub>value of a new ligand molecule against DHDPS.
    BMC Bioinformatics. 01/2010;
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    Article: Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis.
    [show abstract] [hide abstract]
    ABSTRACT: An explosive global spreading of multidrug resistant Mycobacterium tuberculosis (Mtb) is a catastrophe, which demands an urgent need to design or develop novel/potent antitubercular agents. The Lysine/DAP biosynthetic pathway is a promising target due its specific role in cell wall and amino acid biosynthesis. Here, we report identification of potential antitubercular candidates targeting Mtb dihydrodipicolinate synthase (DHDPS) enzyme of the pathway using virtual screening protocols. In the present study, we generated three sets of drug-like molecules in order to screen potential inhibitors against Mtb drug target DHDPS. The first set of compounds was a combinatorial library, which comprised analogues of pyruvate (substrate of DHDPS). The second set of compounds consisted of pyruvate-like molecules i.e. structurally similar to pyruvate, obtained using 3D flexible similarity search against NCI and PubChem database. The third set constituted 3847 anti-infective molecules obtained from PubChem. These compounds were subjected to Lipinski's rule of drug-like five filters. Finally, three sets of drug-like compounds i.e. 4088 pyruvate analogues, 2640 pyruvate-like molecules and 1750 anti-infective molecules were docked at the active site of Mtb DHDPS (PDB code: 1XXX used in the molecular docking calculations) to select inhibitors establishing favorable interactions. The above-mentioned virtual screening procedures helped in the identification of several potent candidates that possess inhibitory activity against Mtb DHDPS. Therefore, these novel scaffolds/candidates which could have the potential to inhibit Mtb DHDPS enzyme would represent promising starting points as lead compounds and certainly aid the experimental designing of antituberculars in lesser time.
    BMC Bioinformatics 01/2010; 11 Suppl 1:S53. · 2.75 Impact Factor
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    Article: ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins.
    Aarti Garg, Gajendra P S Raghava
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    ABSTRACT: The expansion of raw protein sequence databases in the post genomic era and availability of fresh annotated sequences for major localizations particularly motivated us to introduce a new improved version of our previously forged eukaryotic subcellular localizations prediction method namely "ESLpred". Since, subcellular localization of a protein offers essential clues about its functioning, hence, availability of localization predictor would definitely aid and expedite the protein deciphering studies. However, robustness of a predictor is highly dependent on the superiority of dataset and extracted protein attributes; hence, it becomes imperative to improve the performance of presently available method using latest dataset and crucial input features. Here, we describe augmentation in the prediction performance obtained for our most popular ESLpred method using new crucial features as an input to Support Vector Machine (SVM). In addition, recently available, highly non-redundant dataset encompassing three kingdoms specific protein sequence sets; 1198 fungi sequences, 2597 from animal and 491 plant sequences were also included in the present study. First, using the evolutionary information in the form of profile composition along with whole and N-terminal sequence composition as an input feature vector of 440 dimensions, overall accuracies of 72.7, 75.8 and 74.5% were achieved respectively after five-fold cross-validation. Further, enhancement in performance was observed when similarity search based results were coupled with whole and N-terminal sequence composition along with profile composition by yielding overall accuracies of 75.9, 80.8, 76.6% respectively; best accuracies reported till date on the same datasets. These results provide confidence about the reliability and accurate prediction of SVM modules generated in the present study using sequence and profile compositions along with similarity search based results. The presently developed modules are implemented as web server "ESLpred2" available at http://www.imtech.res.in/raghava/eslpred2/.
    BMC Bioinformatics 12/2008; 9:503. · 2.75 Impact Factor
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    Article: DPROT: prediction of disordered proteins using evolutionary information.
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    ABSTRACT: The association of structurally disordered proteins with a number of diseases has engendered enormous interest and therefore demands a prediction method that would facilitate their expeditious study at molecular level. The present study describes the development of a computational method for predicting disordered proteins using sequence and profile compositions as input features for the training of SVM models. First, we developed the amino acid and dipeptide compositions based SVM modules which yielded sensitivities of 75.6 and 73.2% along with Matthew's Correlation Coefficient (MCC) values of 0.75 and 0.60, respectively. In addition, the use of predicted secondary structure content (coil, sheet and helices) in the form of composition values attained a sensitivity of 76.8% and MCC value of 0.77. Finally, the training of SVM models using evolutionary information hidden in the multiple sequence alignment profile improved the prediction performance by achieving a sensitivity value of 78% and MCC of 0.78. Furthermore, when evaluated on an independent dataset of partially disordered proteins, the same SVM module provided a correct prediction rate of 86.6%. Based on the above study, a web server ("DPROT") was developed for the prediction of disordered proteins, which is available at http://www.imtech.res.in/raghava/dprot/.
    Amino Acids 05/2008; 35(3):599-605. · 3.25 Impact Factor
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    Article: VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens.
    Aarti Garg, Dinesh Gupta
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    ABSTRACT: Prediction of bacterial virulent protein sequences has implications for identification and characterization of novel virulence-associated factors, finding novel drug/vaccine targets against proteins indispensable to pathogenicity, and understanding the complex virulence mechanism in pathogens. In the present study we propose a bacterial virulent protein prediction method based on bi-layer cascade Support Vector Machine (SVM). The first layer SVM classifiers were trained and optimized with different individual protein sequence features like amino acid composition, dipeptide composition (occurrences of the possible pairs of ith and i+1th amino acid residues), higher order dipeptide composition (pairs of ith and i+2nd residues) and Position Specific Iterated BLAST (PSI-BLAST) generated Position Specific Scoring Matrices (PSSM). In addition, a similarity-search based module was also developed using a dataset of virulent and non-virulent proteins as BLAST database. A five-fold cross-validation technique was used for the evaluation of various prediction strategies in this study. The results from the first layer (SVM scores and PSI-BLAST result) were cascaded to the second layer SVM classifier to train and generate the final classifier. The cascade SVM classifier was able to accomplish an accuracy of 81.8%, covering 86% area in the Receiver Operator Characteristic (ROC) plot, better than that of either of the layer one SVM classifiers based on single or multiple sequence features. VirulentPred is a SVM based method to predict bacterial virulent proteins sequences, which can be used to screen virulent proteins in proteomes. Together with experimentally verified virulent proteins, several putative, non annotated and hypothetical protein sequences have been predicted to be high scoring virulent proteins by the prediction method. VirulentPred is available as a freely accessible World Wide Web server - VirulentPred, at http://bioinfo.icgeb.res.in/virulent/.
    BMC Bioinformatics 02/2008; 9:62. · 2.75 Impact Factor
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    Article: A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search.
    Aarti Garg, Gajendra P S Raghava
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    ABSTRACT: Most of the prediction methods for secretory proteins require the presence of a correct N-terminal end of the preprotein for correct classification. As large scale genome sequencing projects sometimes assign the 5'-end of genes incorrectly, many proteins are encoded without the correct N-terminus leading to incorrect prediction. In this study, a systematic attempt has been made to predict secretory proteins irrespective of presence or absence of N-terminal signal peptides (also known as classical and non-classical secreted proteins respectively), using machine-learning techniques; artificial neural network (ANN) and support vector machine (SVM). We trained and tested our methods on a dataset of 3321 secretory and 3654 non-secretory mammalian proteins using five-fold cross-validation technique. First, ANN-based modules have been developed for predicting secretory proteins using 33 physico-chemical properties, amino acid composition and dipeptide composition and achieved accuracies of 73.1%, 76.1% and 77.1%, respectively. Similarly, SVM-based modules using 33 physico-chemical properties, amino acid, and dipeptide composition have been able to achieve accuracies of 77.4%, 79.4% and 79.9%, respectively. In addition, BLAST and PSI-BLAST modules designed for predicting secretory proteins based on similarity search achieved 23.4% and 26.9% accuracy, respectively. Finally, we developed a hybrid-approach by integrating amino acid and dipeptide composition based SVM modules and PSI-BLAST module that increased the accuracy to 83.2%, which is significantly better than individual modules. We also achieved high sensitivity of 60.4% with low value of 5% false positive predictions using hybrid module. A web server SRTpred has been developed based on above study for predicting classical and non-classical secreted proteins from whole sequence of mammalian proteins, which is available from http://www.imtech.res.in/raghava/srtpred/.
    In silico biology 02/2008; 8(2):129-40.
  • Article: Further evidence of centrophenoxine mediated protection in aluminium exposed rats by biochemical and light microscopy analysis.
    Bimla Nehru, Punita Bhalla, Aarti Garg
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    ABSTRACT: The environmental agent aluminium has been intensively investigated in the initiation and progression of various neurological disorders and the role of oxidative stress in these disorders is a widely discussed phenomenon. In this light, the present study is focused on the role of aluminium in mediating oxidative stress, which may help in better understanding its role in neuronal degeneration. Further, we have exploited a known anti-aging drug centrophenoxine to explore its potential in the conditions of metal induced oxidative damage. Aluminium was administered orally at a dose level of 100 mg/kg b.wt./day for a period of 6 weeks followed by a post treatment of centrophenoxine at a dose level of 100 mg/kg b.wt./day for another 6 weeks. Following aluminium exposure, a significant increase in lipid peroxidation levels (estimated by MDA) were observed which was accompanied by a decrease in reduced glutathione content in both cerebrum and cerebellum of rat brain. Post treatment of centrophenoxine significantly reduced the lipid peroxidation levels and also increased the reduced glutathione content in both the regions. Histologically observed marked deteriorations in the organization of various cellular layers in both cerebrum and cerebellum were observed after aluminium administration. Centrophenoxine treated animals showed an appreciable improvement in the histoarchitecture of the cellular layers. Our results indicate that centrophenoxine has an antioxidant potential and should be examined further in aluminium toxic conditions.
    Food and Chemical Toxicology 01/2008; 45(12):2499-505. · 3.00 Impact Factor
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    Article: Oxypred: prediction and classification of oxygen-binding proteins.
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    ABSTRACT: This study describes a method for predicting and classifying oxygen-binding proteins. Firstly, support vector machine (SVM) modules were developed using amino acid composition and dipeptide composition for predicting oxygen-binding proteins, and achieved maximum accuracy of 85.5% and 87.8%, respectively. Secondly, an SVM module was developed based on amino acid composition, classifying the predicted oxygen-binding proteins into six classes with accuracy of 95.8%, 97.5%, 97.5%, 96.9%, 99.4%, and 96.0% for erythrocruorin, hemerythrin, hemocyanin, hemoglobin, leghemoglobin, and myoglobin proteins, respectively. Finally, an SVM module was developed using dipeptide composition for classifying the oxygen-binding proteins, and achieved maximum accuracy of 96.1%, 98.7%, 98.7%, 85.6%, 99.6%, and 93.3% for the above six classes, respectively. All modules were trained and tested by five-fold cross validation. Based on the above approach, a web server Oxypred was developed for predicting and classifying oxygen-binding proteins (available from http://www.imtech.res.in/raghava/oxypred/).
    Genomics Proteomics & Bioinformatics 01/2008; 5(3-4):250-2.
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    Article: PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides.
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    ABSTRACT: Among secondary structure elements, beta-turns are ubiquitous and major feature of bioactive peptides. We analyzed 77 biologically active peptides with length varying from 9 to 20 residues. Out of 77 peptides, 58 peptides were found to contain at least one beta-turn. Further, at the residue level, 34.9% of total peptide residues were found to be in beta-turns, higher than the number of helical (32.3%) and beta-sheet residues (6.9%). So, we utilized the predicted beta-turns information to develop an improved method for predicting the three-dimensional (3D) structure of small peptides. In principle, we built four different structural models for each peptide. The first 'model I' was built by assigning all the peptide residues an extended conformation (phi = Psi = 180 degrees ). Second 'model II' was built using the information of regular secondary structures (helices, beta-strands and coil) predicted from PSIPRED. In third 'model III', secondary structure information including beta-turn types predicted from BetaTurns method was used. The fourth 'model IV' had main-chain phi, Psi angles of model III and side chain angles assigned using standard Dunbrack backbone dependent rotamer library. These models were further refined using AMBER package and the resultant C(alpha) rmsd values were calculated. It was found that adding the beta-turns to the regular secondary structures greatly reduces the rmsd values both before and after the energy minimization. Hence, the results indicate that regular and irregular secondary structures, particularly beta-turns information can provide valuable and vital information in the tertiary structure prediction of small bioactive peptides. Based on the above study, a web server PEPstr (http://www.imtech.res.in/raghava/pepstr/) was developed for predicting the tertiary structure of small bioactive peptides.
    Protein and Peptide Letters 02/2007; 14(7):626-31. · 1.94 Impact Factor
  • Article: Evidence for centrophenoxine as a protective drug in aluminium induced behavioral and biochemical alteration in rat brain.
    Bimla Nehru, Punita Bhalla, Aarti Garg
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    ABSTRACT: Potential use of various nootropic drugs have been a burning area of research on account of various physical and chemical insult in brain under different toxicological conditions. One of the nootropic drug centrophenoxine, also known as an anti-aging drug has been exploited in the present experiment under aluminium toxic conditions. Aluminium was administered by oral gavage at a dose level of 100 mg/Kg x b x wt/day for a period of six weeks. To elucidate the region specific response, study was carried out in two different regions of brain namely cerebrum and cerebellum. Following aluminium exposure, a significant decrease in the activities of enzymes namely Hexokinase, Lactate dehydrogenase, Succinate dehydrogenase, Mg(2+) dependent ATPase was observed in both the regions. Moreover, the activity of acetylcholinesterase was also reported to be significantly decreased. Post-treatment with centrophenoxine was able to restore the altered enzyme activities and the effect was observed in both the regions of brain although the activity of lactate dehydrogenase and acetylcholinesterase did not register significant increase in the cerebellum region. Further, centrophenoxine was able to improve the altered short-term memory and cognitive performance resulted from aluminium exposure. From the present study, it can be concluded that centrophenoxine has a potential and can be exploited in other toxicological conditions also.
    Molecular and Cellular Biochemistry 11/2006; 290(1-2):33-42. · 2.06 Impact Factor
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    Article: Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure.
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    ABSTRACT: The present study is an attempt to develop a neural network-based method for predicting the real value of solvent accessibility from the sequence using evolutionary information in the form of multiple sequence alignment. In this method, two feed-forward networks with a single hidden layer have been trained with standard back-propagation as a learning algorithm. The Pearson's correlation coefficient increases from 0.53 to 0.63, and mean absolute error decreases from 18.2 to 16% when multiple-sequence alignment obtained from PSI-BLAST is used as input instead of a single sequence. The performance of the method further improves from a correlation coefficient of 0.63 to 0.67 when secondary structure information predicted by PSIPRED is incorporated in the prediction. The final network yields a mean absolute error value of 15.2% between the experimental and predicted values, when tested on two different nonhomologous and nonredundant datasets of varying sizes. The method consists of two steps: (1) in the first step, a sequence-to-structure network is trained with the multiple alignment profiles in the form of PSI-BLAST-generated position-specific scoring matrices, and (2) in the second step, the output obtained from the first network and PSIPRED-predicted secondary structure information is used as an input to the second structure-to-structure network. Based on the present study, a server SARpred (http://www.imtech.res.in/raghava/sarpred/) has been developed that predicts the real value of solvent accessibility of residues for a given protein sequence. We have also evaluated the performance of SARpred on 47 proteins used in CASP6 and achieved a correlation coefficient of 0.68 and a MAE of 15.9% between predicted and observed values.
    Proteins Structure Function and Bioinformatics 12/2005; 61(2):318-24. · 3.39 Impact Factor
  • Article: Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
    [show abstract] [hide abstract]
    ABSTRACT: The present study is an attempt to develop a neural network-based method for predicting the real value of solvent accessibility from the sequence using evolutionary information in the form of multiple sequence alignment. In this method, two feed-forward networks with a single hidden layer have been trained with standard back-propagation as a learning algorithm. The Pearson's correlation coefficient increases from 0.53 to 0.63, and mean absolute error decreases from 18.2 to 16% when multiple-sequence alignment obtained from PSI-BLAST is used as input instead of a single sequence. The performance of the method further improves from a correlation coefficient of 0.63 to 0.67 when secondary structure information predicted by PSIPRED is incorporated in the prediction. The final network yields a mean absolute error value of 15.2% between the experimental and predicted values, when tested on two different nonhomologous and nonredundant datasets of varying sizes. The method consists of two steps: (1) in the first step, a sequence-to-structure network is trained with the multiple alignment profiles in the form of PSI-BLAST-generated position-specific scoring matrices, and (2) in the second step, the output obtained from the first network and PSIPRED-predicted secondary structure information is used as an input to the second structure-to-structure network. Based on the present study, a server SARpred (http://www.imtech.res.in/raghava/sarpred/) has been developed that predicts the real value of solvent accessibility of residues for a given protein sequence. We have also evaluated the performance of SARpred on 47 proteins used in CASP6 and achieved a correlation coefficient of 0.68 and a MAE of 15.9% between predicted and observed values. Proteins 2005. © 2005 Wiley-Liss, Inc.
    Proteins Structure Function and Bioinformatics 10/2005; 61(2):318 - 324. · 3.39 Impact Factor
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    Article: PSLpred: prediction of subcellular localization of bacterial proteins.
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    ABSTRACT: We developed a web server PSLpred for predicting subcellular localization of gram-negative bacterial proteins with an overall accuracy of 91.2%. PSLpred is a hybrid approach-based method that integrates PSI-BLAST and three SVM modules based on compositions of residues, dipeptides and physico-chemical properties. The prediction accuracies of 90.7, 86.8, 90.3, 95.2 and 90.6% were attained for cytoplasmic, extracellular, inner-membrane, outer-membrane and periplasmic proteins, respectively. Furthermore, PSLpred was able to predict approximately 74% of sequences with an average prediction accuracy of 98% at RI = 5. AVAILABILITY: PSLpred is available at http://www.imtech.res.in/raghava/pslpred/
    Bioinformatics 06/2005; 21(10):2522-4. · 5.47 Impact Factor
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    Article: Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search.
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    ABSTRACT: Here we report a systematic approach for predicting subcellular localization (cytoplasm, mitochondrial, nuclear, and plasma membrane) of human proteins. First, support vector machine (SVM)-based modules for predicting subcellular localization using traditional amino acid and dipeptide (i + 1) composition achieved overall accuracy of 76.6 and 77.8%, respectively. PSI-BLAST, when carried out using a similarity-based search against a nonredundant data base of experimentally annotated proteins, yielded 73.3% accuracy. To gain further insight, a hybrid module (hybrid1) was developed based on amino acid composition, dipeptide composition, and similarity information and attained better accuracy of 84.9%. In addition, SVM modules based on a different higher order dipeptide i.e. i + 2, i + 3, and i + 4 were also constructed for the prediction of subcellular localization of human proteins, and overall accuracy of 79.7, 77.5, and 77.1% was accomplished, respectively. Furthermore, another SVM module hybrid2 was developed using traditional dipeptide (i + 1) and higher order dipeptide (i + 2, i + 3, and i + 4) compositions, which gave an overall accuracy of 81.3%. We also developed SVM module hybrid3 based on amino acid composition, traditional and higher order dipeptide compositions, and PSI-BLAST output and achieved an overall accuracy of 84.4%. A Web server HSLPred (www.imtech.res.in/raghava/hslpred/ or bioinformatics.uams.edu/raghava/hslpred/) has been designed to predict subcellular localization of human proteins using the above approaches.
    Journal of Biological Chemistry 05/2005; 280(15):14427-32. · 4.77 Impact Factor

Institutions

  • 2011
    • University of Padua
      Padova, Veneto, Italy
  • 2010
    • Bioinformatics Institute of India
      Noida, Uttar Pradesh, India
  • 2005–2010
    • Institute of Microbial Technology
      • Bioinformatics Centre (IMTECH)
      Chandīgarh, Union Territory of Chandigarh, India
  • 2006–2008
    • Panjab University
      • Department of Biophysics
      Chandīgarh, Union Territory of Chandigarh, India