Ity for cysteine-stabilized peptides. In fact, this predictor can be used to predict the antimicrobial activity of several peptide sequences, since they have a regular cysteine pattern. The CS-AMPPred can be helpful for revealing the antimicrobial activity from multifunctional peptides. In addition, it can be useful for a prediction prior to synthesis of some predicted proteins in protein databases. In the future, sequences without antimicrobial activity will be predicted and tested in vitro.Availability and RequirementsA standalone version of CS-AMPPred was developed under the GNU/GPL 3.0 license and it is available for download at ,http://sourceforge.net/projects/csamppred/.. The Naringin web software was developed using 23727046 the programming language PERL and compiled using the PERL Archiving Toolkit. CS-AMPPred runs on any Linux machine and its download is free for academic use; commercial users should contact the authors for license.Supporting InformationData Set S1 The blind data set 1 (BS1) in fasta format. It was composed of 75 sequences randomly selected from each set (PS and NS) totaling 150 sequences. (FAS) Data Set S2 The blind data set 2 (BS2) in fasta format. BS2 is composed of 53 antimicrobial sequences with six cysteine residues extracted from APD and 53 proteins randomly generated predicted as transmembrane proteins [20]. (FAS)AcknowledgmentsWe are grateful to Dr. T. Joachims, from Department of Computer Science of Cornell University (USA), for making the SVM Light available; to Dr. S. Thomas and co-workers, from Biomedical Informatics Centre of Pleuromutilin National Institute for Reserch in Reproductive Health (India), for providing the CAMP models; and to Dr. F. C. Fernandes, form Centro ??de Analises Proteomicas e Bioquimicas of Universidade Catolica de Brasilia ?^ ?(Brazil), for conducting the predictions with the ANFIS network for our benchmarking.CS-AMPPred: The Cysteine-Stabilized AMPs PredictorAuthor ContributionsConceived and designed the experiments: WFP OLF. Performed the experiments: ASP WFP. Analyzed the data: WFP ASP OLF. Contributed reagents/materials/analysis tools: OLF. Wrote the paper: WFP OLF.
Epiretinal membrane (ERM) is a retinal disease resulting in a disturbance of macular vision and predisposing to rhegmatogenous retinal detachment [1], which significantly impair quality of life [2,3]. ERM is characterized by wrinkling or distortion of the macular surface caused by retinal cell migration and proliferation [4?], and it has been associated with a variety of ocular diseases, such as diabetic retinopathy (DR) [7,8], retinal vein occlusion [4,9], retinal detachment [9?1], and cataract surgery [4,5,7?9,12]. Most cases, however, are termed idiopathic ERM (iERM): they have no antecedent ocular pathology other than posterior vitreous detachment (PVD) or separation [13,14]. While the pathogenesis of iERM is not fully clear, there is growing evidence that PVD plays a critical role in the pathogenesis of iERM through at least two possible mechanisms [15]. First, transient vitreoretinal traction during the development of PVD may cause dehiscences in the internal limiting membrane (ILM) through which glial cells can migrate and proliferate on the inner retinal surface [16?8].Second, and perhaps more frequently, iERM may result from the proliferation and transdifferentiation of hyalocytes contained within vitreous cortical remnants left on the retinal surface following PVD [19?1]. Epidemiological studies contribute to clarify the pathogenesis.Ity for cysteine-stabilized peptides. In fact, this predictor can be used to predict the antimicrobial activity of several peptide sequences, since they have a regular cysteine pattern. The CS-AMPPred can be helpful for revealing the antimicrobial activity from multifunctional peptides. In addition, it can be useful for a prediction prior to synthesis of some predicted proteins in protein databases. In the future, sequences without antimicrobial activity will be predicted and tested in vitro.Availability and RequirementsA standalone version of CS-AMPPred was developed under the GNU/GPL 3.0 license and it is available for download at ,http://sourceforge.net/projects/csamppred/.. The software was developed using 23727046 the programming language PERL and compiled using the PERL Archiving Toolkit. CS-AMPPred runs on any Linux machine and its download is free for academic use; commercial users should contact the authors for license.Supporting InformationData Set S1 The blind data set 1 (BS1) in fasta format. It was composed of 75 sequences randomly selected from each set (PS and NS) totaling 150 sequences. (FAS) Data Set S2 The blind data set 2 (BS2) in fasta format. BS2 is composed of 53 antimicrobial sequences with six cysteine residues extracted from APD and 53 proteins randomly generated predicted as transmembrane proteins [20]. (FAS)AcknowledgmentsWe are grateful to Dr. T. Joachims, from Department of Computer Science of Cornell University (USA), for making the SVM Light available; to Dr. S. Thomas and co-workers, from Biomedical Informatics Centre of National Institute for Reserch in Reproductive Health (India), for providing the CAMP models; and to Dr. F. C. Fernandes, form Centro ??de Analises Proteomicas e Bioquimicas of Universidade Catolica de Brasilia ?^ ?(Brazil), for conducting the predictions with the ANFIS network for our benchmarking.CS-AMPPred: The Cysteine-Stabilized AMPs PredictorAuthor ContributionsConceived and designed the experiments: WFP OLF. Performed the experiments: ASP WFP. Analyzed the data: WFP ASP OLF. Contributed reagents/materials/analysis tools: OLF. Wrote the paper: WFP OLF.
Epiretinal membrane (ERM) is a retinal disease resulting in a disturbance of macular vision and predisposing to rhegmatogenous retinal detachment [1], which significantly impair quality of life [2,3]. ERM is characterized by wrinkling or distortion of the macular surface caused by retinal cell migration and proliferation [4?], and it has been associated with a variety of ocular diseases, such as diabetic retinopathy (DR) [7,8], retinal vein occlusion [4,9], retinal detachment [9?1], and cataract surgery [4,5,7?9,12]. Most cases, however, are termed idiopathic ERM (iERM): they have no antecedent ocular pathology other than posterior vitreous detachment (PVD) or separation [13,14]. While the pathogenesis of iERM is not fully clear, there is growing evidence that PVD plays a critical role in the pathogenesis of iERM through at least two possible mechanisms [15]. First, transient vitreoretinal traction during the development of PVD may cause dehiscences in the internal limiting membrane (ILM) through which glial cells can migrate and proliferate on the inner retinal surface [16?8].Second, and perhaps more frequently, iERM may result from the proliferation and transdifferentiation of hyalocytes contained within vitreous cortical remnants left on the retinal surface following PVD [19?1]. Epidemiological studies contribute to clarify the pathogenesis.
