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Computational proteomics
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Ebook "Functional coherence of molecular networks in bioinformatics" will provide a detailed review of existing knowledge on the functional characterization of biological networks. In 15 chapters authored by an international group of prolific systems biology and bioinformatics researchers, it will organize, conceptualize, and summarize the existing core of research results and computational methods on understanding biological function from a network perspective.
235p
ladongphongthanh1008
22-04-2024
5
3
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p
vicwell
29-02-2024
5
2
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To understand diversity in enormous collections of genome sequences, we need computationally scalable tools that can quickly contextualize individual genomes based on their similarities and identify features of each genome that make them unique.
6p
viarchimedes
26-01-2022
7
0
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Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succinylation of lysine residues has recently attracted the interest of the scientific community. The experimental detection of succinylation sites is an expensive process, which consumes a lot of time and resources. Therefore, computational predictors of this covalent modification have emerged as a last resort to tackling lysine succinylation.
10p
vilarryellison
29-10-2021
9
0
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Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach.
21p
viansan2711
30-07-2021
9
1
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Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome.
11p
viwyoming2711
16-12-2020
13
0
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Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.
18p
vikentucky2711
26-11-2020
10
0
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Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge.
11p
vikentucky2711
26-11-2020
6
0
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Human T-cell leukemia viruses (HTLV) tend to induce some fatal human diseases like Adult T-cell Leukemia (ATL) by targeting human T lymphocytes. To indentify the protein-protein interactions (PPI) between HTLV viruses and Homo sapiens is one of the significant approaches to reveal the underlying mechanism of HTLV infection and host defence.
10p
vikentucky2711
26-11-2020
9
1
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Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. Results: On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months.
22p
vikentucky2711
26-11-2020
11
1
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Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets.
8p
vikentucky2711
26-11-2020
19
1
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Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousands, and the number of viral proteins into the hundreds of thousands, we report a systematic computational analysis of the point of first-contact between viruses and their hosts, namely viral transmembrane (TM) proteins.
11p
vioklahoma2711
19-11-2020
7
2
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Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps.
10p
vioklahoma2711
19-11-2020
7
2
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Protein complexes carry out nearly all signaling and functional processes within cells. The study of protein complexes is an effective strategy to analyze cellular functions and biological processes. With the increasing availability of proteomics data, various computational methods have recently been developed to predict protein complexes.
14p
vioklahoma2711
19-11-2020
7
2
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With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour.
7p
vioklahoma2711
19-11-2020
8
1
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Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses.
16p
vioklahoma2711
19-11-2020
12
0
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Computational prediction of protein function constitutes one of the more complex problems in Bioinformatics, because of the diversity of functions and mechanisms in that proteins exert in nature. This issue is reinforced especially for proteins that share very low primary or tertiary structure similarity to existing annotated proteomes.
14p
viflorida2711
30-10-2020
11
2
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Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of druggable genomes.
10p
viflorida2711
30-10-2020
10
2
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Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes.
10p
vicoachella2711
27-10-2020
5
0
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Tandem mass spectrometry (MS/MS)-based database searching is a widely acknowledged and widely used method for peptide identification in shotgun proteomics. However, due to the rapid growth of spectra data produced by advanced mass spectrometry and the greatly increased number of modified and digested peptides identified in recent years.
13p
vijisoo2711
27-10-2020
16
1
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