instruction:
In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
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Background: We present here the recent update of AMS algorithm for identification of post-translational modification (PTM) sites in proteins based only on sequence information, using artificial neural network (ANN) method. The query protein sequence is dissected into overlapping short sequence segments. Ten different physicochemical features describe each amino acid; therefore nine residues long segment is represented as a point in a 90 dimensional space. The database of sequence segments with confirmed by experiments post-translational modification sites are used for training a set of ANNs. The efficiency of the classification for each type of modification and the prediction power of the method is estimated here using recall (sensitivity), precision values, the area under receiver operating characteristic (ROC) curves and leave-one-out tests (LOOCV). The significant differences in the performance for differently optimized neural networks are observed, yet the AMS 3.0 tool integrates those heterogeneous classification schemes into the single consensus scheme, and it is able to boost the precision and recall values independent of a PTM type in comparison with the currently available state-of-the art methods. The standalone version of AMS 3.0 presents an efficient way to indentify post-translational modifications for whole proteomes. The training datasets, precompiled binaries for AMS 3.0 tool and the source code are available at Additional file 1 Supplementary materials for the publication. Supplementary.xls contains detailed results of training and testing of AMS 3.0 tool in MS Excel file format. Additional file 2 PTM predictor software with training data. PTM_Archive.tar.gz includes the predictor software binaries together with all trained ANNs in tar.gz compressed form.
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AMS 3.0: prediction of post-translational modifications


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The presentation of viral peptide epitopes to host cytotoxic T lymphocytes (CTLs) is crucial for adaptive cellular immunity to clear the virus infection, especially for some chronic viral infections. Indeed, hosts have developed effective strategies to achieve this goal. The ideal scenario would be that the peptide epitopes stimulate a broad spectrum of CTL responses with diversified T-cell receptor (TCR) usage (the TCR repertoire). It is believed that a diversified TCR repertoire requires a "featured" peptide to be presented by the host major histocompatibility complex (MHC). A featured peptide can be processed and presented in a number of ways. Here, using the X-ray diffraction method, the crystal structures of an antigenic peptide derived from rinderpest virus presented by bovine MHC class I N*01801 (BoLA-A11) have been solved, and two distinct conformations of the presented peptide are clearly displayed. A detailed analysis of the structure and comparative sequences revealed that the polymorphic amino acid isoleucine 73 (Ile73) is extremely flexible, allowing the MHC groove to adopt different conformations to accommodate the rinderpest virus peptide. This makes the peptide more featured by exposing different amino acids for T-cell recognition. The crystal structures also demonstrated that the N*01801 molecule has an unusually large A pocket, resulting in the special conformation of the P1 residue at the N terminus of the peptide. We propose that this strategy of host peptide presentation might be beneficial for creating a diversified TCR repertoire, which is important for a moreeffective CTL response. Viral diseases and other infections caused by intracellular pathogens of cattle result in large global economic losses every year. In the past several decades, rinderpest virus (RPV) (23, 40), foot-and-mouth disease virus (FMDV) (7), and bovine tuberculosis infection (62) have brought disastrous consequences, including social panic and even a threat to human health. Nearly 6 decades ago, most countries were committed to developing more-effective vaccines (46), and remarkable achievements were made in controlling threatening bovine viral infectious diseases and other zoonoses (23, 46). In the 1960s, British virologist Walter Plowright developed a live attenuated vaccine against rinderpest virus, which was widely used in rinderpest eradication efforts (40). However, it still remains extremely challenging for humans to completely eradicate a virus. The questions of how the bovine attenuated vaccine induces immune responses and how the viral peptides are presented and recognized by host immune molecules are still largely unanswered. Therefore, studies on bovine immunity against the rinderpest virus may provide clues for our battle against other viral infections. Generally speaking, effective vaccines have common characteristics: they are rich in T-cell and B-cell epitopes and can induce the immune system to generate protective immune responses (3, 36, 54) . During this process, major histocompatibility complex (MHC) molecules play a pivotal role in the host. MHC class I (MHC I) molecules form a heterotrimer complex composed of the heavy chain of MHC, the antigenic peptide, and ␤ 2 -microglobulin (␤ 2 m). Generally, MHC I loads endogenous peptides, including the virus-derived peptides. Briefly, at the initial stage of virus infection, antigenic proteins are processed in a proteasome-dependent or -independent manner. The resultant short peptides are then transported to the endoplasmic reticulum and are loaded onto the peptidebinding grooves of MHC I molecules. Consequently, the peptide-loading MHC I complexes are translocated to the cell surface and are recognized by cytotoxic T lymphocytes (CTLs) with specific T-cell receptors (TCRs) (49, 63). This immune recognition induces an MHC-restricted CD8 ϩ T-cell response that is characterized by the killing and elimination of the infected cells by effector T cells. The majority of virus-derived peptides are processed and presented through this pathway
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Two Distinct Conformations of a Rinderpest Virus Epitope Presented by Bovine Major Histocompatibility Complex Class I N*01801: a Host Strategy To Present Featured Peptides ᰔ †


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Acute viral bronchiolitis is a major cause of morbidity and mortality in infants. 1,2 Bronchiolitis, which literally means inflammation of the bronchioles, was first described more than 150 years ago as 'congestive catarrhal fever' to illustrate the clinical pattern of fever, rhinorrhoea, wheezing, crepitations, dyspnoea and difficulty feeding. It was not until 1957 that the epidemiology and viral aetiology were first described. 3 Respiratory syncytial virus (RSV) is the main virus to cause bronchiolitis and is associated with over 75% of cases where a pathogen has been isolated. 4 Other viruses, including
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Innate immune response and bronchiolitis and preschool recurrent wheeze