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7983-2017
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amino acid sequences
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- Author:
- Tobias Fehlmann; Shashwat Sahay; Andreas Keller; Christina Backes
- Source:
- Briefings in bioinformatics 2017 v.20 no.3 pp. 1011-1020
- ISSN:
- 1477-4054
- Subject:
- Internet; amino acid sequences; binding sites; databases; genes; microRNA; nucleotide sequences; patients; precision medicine; prediction; protein synthesis; single nucleotide polymorphism
- Abstract:
- ... Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, i ...
- DOI:
- 10.1093/bib/bbx155
- https://doi.org/10.1093/bib/bbx155
- Author:
- Tzu-Yuan Wang; Cheng-Hong Hsieh; Chuan-Chuan Hung; Chia-Ling Jao; Pei-Yi Lin; You-Liang Hsieh; Kuo-Chiang Hsu
- Source:
- Food chemistry 2017 v.234 pp. 431-438
- ISSN:
- 0308-8146
- Subject:
- amino acid sequences; correlation; databases; dipeptidyl-peptidase IV; peptides; prediction; protein hydrolysates; proteinases
- Abstract:
- ... A total of 294 edible protein sequences and 5 commercial proteases listed in the BIOPEP database were analyzed in silico. The frequency (A), a parameter in silico described previously, was examined further to calculating the ratio of truncated peptides with Xaa-proline and/or Xaa-alanine to all peptide fragments in a protein hydrolyzed with a protease, using the BIOPEP database. Then the in vitro ...
- DOI:
- 10.1016/j.foodchem.2017.05.035
- https://doi.org/10.1016/j.foodchem.2017.05.035
3. Analysis of plant UDP-arabinopyranose mutase (UAM): Role of divalent metals and structure prediction
- Author:
- Jijin R.A. Kuttiyatveetil; David A.R. Sanders
- Source:
- Biochimica et biophysica acta 2017 v.1865 no.5 pp. 510-519
- ISSN:
- 1570-9639
- Subject:
- Arabidopsis thaliana; Hordeum vulgare; Oryza sativa; amino acid sequences; barley; catalytic activity; divalent metals; enzyme activity; genes; glycosylation; manganese; metal ions; models; prediction; proteins; rice; sugars
- Abstract:
- ... UDP-arabinopyranose mutase (UAM) is a plant enzyme which interconverts UDP-arabinopyranose (UDP-Arap; a six-membered sugar) to UDP-arabinofuranose (UDP-Araf; a five-membered sugar). Plant mutases belong to a small gene family called Reversibly Glycosylated Proteins (RGPs). So far, UAM has been identified in Oryza sativa (Rice), Arabidopsis thaliana and Hordeum vulgare (Barley). The enzyme requires ...
- DOI:
- 10.1016/j.bbapap.2017.02.005
- https://doi.org/10.1016/j.bbapap.2017.02.005
4. Computational prediction and analysis of deleterious cancer associated missense mutations in DYNC1H1
- Author:
- Ceren Sucularli; Melda Arslantas
- Source:
- Molecular and cellular probes 2017 v.34 pp. 21-29
- ISSN:
- 0890-8508
- Subject:
- DNA damage; amino acid sequences; amino acid substitution; biomarkers; colorectal neoplasms; databases; dynein ATPase; genes; humans; missense mutation; mitotic spindle apparatus; neurodegenerative diseases; pancreatic neoplasms; prediction; proteins
- Abstract:
- ... Dynein, cytoplasmic 1, heavy chain 1 (DYNC1H1) gene encodes a subunit of human cytoplasmic dynein complex, which has several crucial functions in the cell, such as intracellular transport of DNA damage proteins and mitotic spindle positioning. Recent studies reported the altered expression of DYNC1H1 in different cancers and DYNC1H1 was suggested to be potential biomarker in colorectal cancers. Pr ...
- DOI:
- 10.1016/j.mcp.2017.04.004
- https://doi.org/10.1016/j.mcp.2017.04.004
- Author:
- José Juan Almagro Armenteros; Casper Kaae Sønderby; Søren Kaae Sønderby; Henrik Nielsen; Ole Winther
- Source:
- Bioinformatics 2017 v.33 no.21 pp. 3387-3395
- ISSN:
- 1460-2059
- Subject:
- Internet; algorithms; amino acid sequences; artificial intelligence; bioinformatics; data collection; databases; neural networks; prediction; proteins; proteomics
- Abstract:
- ... The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effec ...
- DOI:
- 10.1093/bioinformatics/btx431
- https://doi.org/10.1093/bioinformatics/btx431
- Author:
- Lingyun Qin; Huili Liu; Rong Chen; Jingjing Zhou; Xiyao Cheng; Yao Chen; Yongqi Huang; Zhengding Su
- Source:
- Biochemistry 2017 v.56 no.44 pp. 5943-5954
- ISSN:
- 1520-4995
- Subject:
- amino acid sequences; binding capacity; chemical interactions; drugs; engineering; ligands; mice; models; molecular dynamics; mutants; oncogene proteins; pharmacology; prediction; protein conformation; protein engineering; screening
- Abstract:
- ... The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays ...
- DOI:
- 10.1021/acs.biochem.7b00903
- https://doi.org/10.1021/acs.biochem.7b00903
- Author:
- Damiano Piovesan; Ian Walsh; Giovanni Minervini; Silvio C.E. Tosatto
- Source:
- Bioinformatics 2017 v.33 no.12 pp. 1889-1891
- ISSN:
- 1460-2059
- Subject:
- Internet; amino acid sequences; bioinformatics; computer software; prediction; proteins
- Abstract:
- ... Motivation: The behavior of a protein is encoded in its sequence, which can be used to predict distinct features such as secondary structure, intrinsic disorder or amphipathicity. Integrating these and other features can help explain the context-dependent behavior of proteins. However, most tools focus on a single aspect, hampering a holistic understanding of protein structure. Here, we present Fa ...
- DOI:
- 10.1093/bioinformatics/btx085
- https://doi.org/10.1093/bioinformatics/btx085
- Author:
- Jie Xu; Yajie Jiang; Lu Wan; Qi Wang; Zebo Huang; Yongmei Liu; Yingliang Wu; Zongyun Chen; Xin Liu
- Source:
- Peptides 2017 v.89 pp. 1-8
- ISSN:
- 0196-9781
- Subject:
- Caenorhabditis elegans; Escherichia coli; Scorpiones; amino acid sequences; analgesia; animal models; animals; epilepsy; fecundity; gene expression; gene expression regulation; glutathione transferase; locomotion; longevity; microarray technology; mutants; neoplasms; polyacrylamide gel electrophoresis; polypeptides; prediction; quantitative analysis; quantitative polymerase chain reaction; venoms
- Abstract:
- ... Scorpion venom could be a useful treatment for a variety of diseases, such as cancer, epilepsy and analgesia. BmKTX is a polypeptide extracts from scorpion venom (PESV), which have attracted much attention from researchers in recent years. mBmKTX is a mutant polypeptide according to the amino acid sequence of BmKTX. We expressed it with the vector pGEX-4T-1 in Escherichia coli, and Caenorhabditis ...
- DOI:
- 10.1016/j.peptides.2017.01.003
- https://doi.org/10.1016/j.peptides.2017.01.003
- Author:
- Dazhi Jiao; Wontack Han; Yuzhen Ye
- Source:
- Methods 2017 v.129 pp. 8-17
- ISSN:
- 1046-2023
- Subject:
- DNA; amino acid sequences; genes; metagenomics; microbial communities; nucleotide sequences; phylogeny; prediction; proteins
- Abstract:
- ... Recent years have witnessed unprecedented accumulation of DNA sequences and therefore protein sequences (predicted from DNA sequences), due to the advances of sequencing technology. One of the major sources of the hypothetical proteins is the metagenomics research. Current annotation of metagenomes (collections of short metagenomic sequences or assemblies) relies on similarity searches against kno ...
- DOI:
- 10.1016/j.ymeth.2017.04.018
- PubMed:
- 28454776
- PubMed Central:
- PMC5643221
- https://doi.org/10.1016/j.ymeth.2017.04.018
- Author:
- Manimekalai Ramaswamy; Jini Narayanan; Gokul Manickavachagam; Selvi Athiappan; Meena Arun; Gomathi R; Bakshi Ram
- Source:
- Agri Gene 2017 v.3 pp. 1-11
- ISSN:
- 2352-2151
- Subject:
- Arabidopsis; Sorghum bicolor; alanine; amino acid sequences; corn; genes; grasses; leucine; phylogeny; prediction; proline; rice; sequence analysis; sugarcane
- Abstract:
- ... A total of 85 NAC genes of sugarcane (ScNAC) were retrieved from GRASSIUS (grass regulatory information server). An overview of this gene family is presented including conserved domains, phylogenies, comparative analysis of NAC genes of sugarcane with its closest relative sorghum and with other monocot species. Among the Poaceae family, the NAC genes from sugarcane showed high sequence identity wi ...
- DOI:
- 10.1016/j.aggene.2016.10.003
- https://doi.org/10.1016/j.aggene.2016.10.003
- Author:
- Hang Zhou; Yang Yang; Hong-Bin Shen
- Source:
- Bioinformatics 2017 v.33 no.6 pp. 843-853
- ISSN:
- 1460-2059
- Subject:
- algorithms; amino acid sequences; amino acids; artificial intelligence; bioinformatics; data collection; gene ontology; humans; models; prediction; proteins; proteome
- Abstract:
- ... Motivation: Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where statistical machine learning algorithms are widely used for model construction. A key step in these predictors is encoding the amino acid sequences into f ...
- DOI:
- 10.1093/bioinformatics/btw723
- https://doi.org/10.1093/bioinformatics/btw723
- Author:
- Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
- Source:
- Bioinformatics 2017 v.33 no.11 pp. 1656-1663
- ISSN:
- 1460-2059
- Subject:
- amino acid sequences; artificial intelligence; bioinformatics; data collection; models; prediction; protein-protein interactions
- Abstract:
- ... Motivation: The identification of protein–protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge. Results: We present ISPRED4, an improved structure-based predictor of PPI ...
- DOI:
- 10.1093/bioinformatics/btx044
- https://doi.org/10.1093/bioinformatics/btx044
- Author:
- Arina Gromova; Hongxing Zhao; Anne Konzer; Alexander Falk; Ulf Pettersson; Sara Bergström Lind
- Source:
- Virus research 2017 v.238 pp. 110-113
- ISSN:
- 0168-1702
- Subject:
- Adenoviridae; amino acid sequences; arginine; bioinformatics; genes; mass spectrometry; messenger RNA; prediction; proteomics; serine; transcription (genetics)
- Abstract:
- ... A hitherto predicted but undetected protein, C-168, in adenovirus type 2 (Ad2) has been identified using mass spectrometry (MS) based proteomics. The gene of this 17.7kDa protein is located on the forward strand in the major late transcription unit between base pairs 9294 and 9797. A tryptic peptide, derived from the C-terminal part of the protein, was identified with high amino acid sequence cove ...
- DOI:
- 10.1016/j.virusres.2017.06.013
- https://doi.org/10.1016/j.virusres.2017.06.013
- Author:
- H.T. Dong; S. Jitrakorn; P. Kayansamruaj; N. Pirarat; C. Rodkhum; T. Rattanarojpong; S. Senapin; V. Saksmerprome
- Source:
- Fish & shellfish immunology 2017 v.68 pp. 65-73
- ISSN:
- 1050-4648
- Subject:
- Infectious spleen and kidney necrosis virus; Lates calcarifer; amino acid sequences; brain; coat proteins; disease prevention; epitopes; farmers; farms; genes; genotype; histology; in situ hybridization; kidneys; liver; marine fish; models; necrosis; nucleotide sequences; pancreas; polymerase chain reaction; prediction; sequence analysis; spleen; vaccines; viruses; Vietnam
- Abstract:
- ... Emergence of a disease with clinical signs resembling megalocytivirus infection seriously affected large-scale barramundi farms in Vietnam in 2012–2014 with estimated losses reaching $435,810 per year. An oil-based, inactivated vaccine against red sea bream iridovirus (RSIV) was applied in one farm for disease prevention without analysis of the causative agent, and the farmer reported inadequate p ...
- DOI:
- 10.1016/j.fsi.2017.06.054
- https://doi.org/10.1016/j.fsi.2017.06.054
- Author:
- Diego J. Zea; Diego Anfossi; Morten Nielsen; Cristina Marino-Buslje
- Source:
- Bioinformatics 2017 v.33 no.4 pp. 564-565
- ISSN:
- 1460-2059
- Subject:
- amino acid sequences; bioinformatics; computer software; prediction; sequence alignment
- Abstract:
- ... Motivation: MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward. MIToS streamlines the implementation of any measure calculated from residue contingency tables and it ...
- DOI:
- 10.1093/bioinformatics/btw646
- https://doi.org/10.1093/bioinformatics/btw646
- Author:
- Liani Coronado; Matthias Liniger; Sara Muñoz-González; Alexander Postel; Lester Josue Pérez; Marta Pérez-Simó; Carmen Laura Perera; Maria Teresa Frías- Lepoureau; Rosa Rosell; Adam Grundhoff; Daniela Indenbirken; Malik Alawi; Nicole Fischer; Paul Becher; Nicolas Ruggli; Llilianne Ganges
- Source:
- Veterinary microbiology 2017 v.201 pp. 103-112
- ISSN:
- 0378-1135
- Subject:
- 3' untranslated regions; Classical swine fever virus; amino acid sequences; amino acid substitution; amino acids; chronic diseases; feeder pigs; hog cholera; immunization; inoculum; neonates; piglets; prediction; rabbits; viral proteins; virulence; viruses
- Abstract:
- ... In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persisten ...
- DOI:
- 10.1016/j.vetmic.2017.01.013
- https://doi.org/10.1016/j.vetmic.2017.01.013
- Author:
- Shan-Shan Hu; Peng Chen; Bing Wang; Jinyan Li
- Source:
- Amino acids 2017 v.49 no.10 pp. 1773-1785
- ISSN:
- 0939-4451
- Subject:
- algorithms; amino acid sequences; amino acids; artificial intelligence; binding proteins; databases; drugs; models; prediction; surface area
- Abstract:
- ... Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thu ...
- DOI:
- 10.1007/s00726-017-2474-6
- https://doi.org/10.1007/s00726-017-2474-6
- Author:
- Xiaoli Zhang; Shiyong Liu
- Source:
- Bioinformatics 2017 v.33 no.6 pp. 854-862
- ISSN:
- 1460-2059
- Subject:
- RNA-binding proteins; amino acid sequences; bioinformatics; experimental design; humans; physicochemical properties; prediction; proteome; support vector machines
- Abstract:
- ... Motivation: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computational prediction is much more efficient than experimental methods and may have guiding significance on the experiment design. Results: In this study, we p ...
- DOI:
- 10.1093/bioinformatics/btw730
- https://doi.org/10.1093/bioinformatics/btw730
- Author:
- Hamidreza Kavianpour; Mahdi Vasighi
- Source:
- Amino acids 2017 v.49 no.2 pp. 261-271
- ISSN:
- 0939-4451
- Subject:
- amino acid sequences; amino acids; data collection; databases; hydrophobicity; models; molecular biology; prediction; proteins; support vector machines; texture
- Abstract:
- ... Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational method ...
- DOI:
- 10.1007/s00726-016-2354-5
- https://doi.org/10.1007/s00726-016-2354-5
20. What are the structural features that drive partitioning of proteins in aqueous two-phase systems?
- Author:
- Zhonghua Wu; Gang Hu; Kui Wang; Boris Yu. Zaslavsky; Lukasz Kurgan; Vladimir N. Uversky
- Source:
- Biochimica et biophysica acta 2017 v.1865 no.1 pp. 113-120
- ISSN:
- 1570-9639
- Subject:
- amino acid sequences; crystal structure; models; prediction; structural proteins
- Abstract:
- ... Protein partitioning in aqueous two-phase systems (ATPSs) represents a convenient, inexpensive, and easy to scale-up protein separation technique. Since partition behavior of a protein dramatically depends on an ATPS composition, it would be highly beneficial to have reliable means for (even qualitative) prediction of partitioning of a target protein under different conditions. Our aim was to unde ...
- DOI:
- 10.1016/j.bbapap.2016.09.010
- https://doi.org/10.1016/j.bbapap.2016.09.010
- Author:
- Xiang Cheng; Shu-Guang Zhao; Wei-Zhong Lin; Xuan Xiao; Kuo-Chen Chou
- Source:
- Bioinformatics 2017 v.33 no.22 pp. 3524-3531
- ISSN:
- 1460-2059
- Subject:
- amino acid sequences; animal proteins; bioinformatics; computational methodology; data collection; mathematics; organelles; prediction; reproduction
- Abstract:
- ... Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy t ...
- DOI:
- 10.1093/bioinformatics/btx476
- https://doi.org/10.1093/bioinformatics/btx476
- Author:
- Xiang Cheng; Xuan Xiao; Kuo-Chen Chou
- Source:
- Gene 2017 v.628 pp. 315-321
- ISSN:
- 0378-1119
- Subject:
- amino acid composition; amino acid sequences; data collection; drugs; gene ontology; mathematics; prediction; scientists; viral proteins
- Abstract:
- ... Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Alt ...
- DOI:
- 10.1016/j.gene.2017.07.036
- https://doi.org/10.1016/j.gene.2017.07.036
23. A new hybrid coding for protein secondary structure prediction based on primary structure similarity
- Author:
- Zhong Li; Jing Wang; Shunpu Zhang; Qifeng Zhang; Wuming Wu
- Source:
- Gene 2017 v.618 pp. 8-13
- ISSN:
- 0378-1119
- Subject:
- amino acid sequences; amino acids; hybrids; physicochemical properties; prediction; principal component analysis; protein secondary structure; support vector machines
- Abstract:
- ... The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the physicochemical properties of amino acids to cons ...
- DOI:
- 10.1016/j.gene.2017.03.011
- https://doi.org/10.1016/j.gene.2017.03.011
- Author:
- Yu Wang; Yanzhi Guo; Xuemei Pu; Menglong Li
- Source:
- RSC advances 2017 v.7 no.31 pp. 18937-18945
- ISSN:
- 2046-2069
- Subject:
- amino acid composition; amino acid sequences; data collection; experimental design; prediction; proteins; support vector machines
- Abstract:
- ... Molecular recognition features (MoRFs) are relatively short segments (10–70 residues) within intrinsically disordered regions (IDRs) that can undergo disorder-to-order transitions during binding to partner proteins. Since MoRFs play key roles in important biological processes such as signaling and regulation, identifying them is crucial for a full understanding of the functional aspects of the IDR ...
- DOI:
- 10.1039/c6ra27161h
- https://doi.org/10.1039/c6ra27161h
- Author:
- Jung-Kil Seo; Dong-Gyun Kim; Ryunkyoung Oh; Kwon-Sam Park; In-Ah Lee; Sang-Man Cho; Ki–Young Lee; Bo-Hye Nam
- Source:
- Fish & shellfish immunology 2017 v.67 pp. 675-683
- ISSN:
- 1050-4648
- Subject:
- 5' untranslated regions; Crassostrea gigas; amino acid sequences; amino acids; antimicrobial peptides; antimicrobial properties; aquatic invertebrates; cation exchange; complementary DNA; gene expression; models; molecular weight; open reading frames; prediction; reversed-phase high performance liquid chromatography; ribosomal proteins; tissue distribution
- Abstract:
- ... We purified an ∼6.4-kDa antimicrobial peptide from an acidified gill extract of the Pacific oyster, Crassostrea gigas, by cation-exchange and C18 reversed-phase high performance liquid chromatography (HPLC). The identified peptide was composed of 54 amino acids and had a molecular weight of 6484.6 Da. Comparison of the amino acid sequence and molecular weight with those of other known proteins or ...
- DOI:
- 10.1016/j.fsi.2017.06.058
- https://doi.org/10.1016/j.fsi.2017.06.058
- Author:
- Scott McClain
- Source:
- Molecular nutrition & food research 2017 v.61 no.8 pp. -
- ISSN:
- 1613-4125
- Subject:
- Betula; algorithms; allergens; amino acid sequences; bioinformatics; cross reaction; databases; epitopes; immunoglobulin E; peanuts; pollen; prediction; screening; shrimp; trees; tropomyosins
- Abstract:
- ... Protein allergens can be related by cross‐reactivity. Allergens that share relevant sequence can cross‐react, those lacking sufficient similarity in their IgE antibody‐binding epitopes do not cross‐react. Cross‐reactivity is based on shared epitopes that is based on shared sequence and higher level structure (charge and shape). Epitopes are important in predicting cross‐reactivity potential and ma ...
- DOI:
- 10.1002/mnfr.201600676
- PubMed:
- 28191711
- PubMed Central:
- PMC5573986
- https://doi.org/10.1002/mnfr.201600676
27. Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica
- Author:
- Zhongying Qiu; Fei Liu; Huimeng Lu; Yuan Huang
- Source:
- Molecular ecology resources 2017 v.17 no.3 pp. 381-392
- ISSN:
- 1755-098X
- Subject:
- Tetrix; adults; amino acid sequences; color; computer software; gene expression; gene ontology; genomics; insects; juvenile hormones; larvae; metabolism; microsatellite repeats; prediction; signal transduction; single nucleotide polymorphism; transcriptome; transcriptomics; unigenes
- Abstract:
- ... The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better un ...
- DOI:
- 10.1111/1755-0998.12553
- https://doi.org/10.1111/1755-0998.12553
- Author:
- Behnaz Deihim; Malihe Hassanzadeh; Nazanin Zahra Shafiei-Jandaghi; Massoud Amanlou; Masoumeh Douraghi
- Source:
- Microbial pathogenesis 2017 v.113 pp. 74-84
- ISSN:
- 0882-4010
- Subject:
- Acinetobacter baumannii; DNA repair; adenosine triphosphate; amino acid sequences; bacteria; base pair mismatch; computer software; dimerization; genes; hydrolysis; missense mutation; models; molecular cloning; nucleotide sequences; phenotype; polymerase chain reaction; prediction; proteins; sequence analysis
- Abstract:
- ... Mutations of mutS and mutL genes have been linked with the emergence of hypermutator (HPM) phenotype in several bacteria. Nevertheless, there is scarce evidence that these mutations occurred in HPM Acinetobacter baumannii, therefore, it remains unknown whether the mutations located in domains mediating the functions of MutS and MutL. To address this information gap, the nucleotide sequences of mut ...
- DOI:
- 10.1016/j.micpath.2017.10.001
- https://doi.org/10.1016/j.micpath.2017.10.001
29. Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions
- Author:
- Fanchi Meng; Vladimir N. Uversky; Lukasz Kurgan
- Source:
- Cellular and molecular life sciences 2017 v.74 no.17 pp. 3069-3090
- ISSN:
- 1420-682X
- Subject:
- Internet; amino acid sequences; databases; models; prediction; proteins
- Abstract:
- ... Computational prediction of intrinsic disorder in protein sequences dates back to late 1970 and has flourished in the last two decades. We provide a brief historical overview, and we review over 30 recent predictors of disorder. We are the first to also cover predictors of molecular functions of disorder, including 13 methods that focus on disordered linkers and disordered protein–protein, protein ...
- DOI:
- 10.1007/s00018-017-2555-4
- https://doi.org/10.1007/s00018-017-2555-4
30. Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity
- Author:
- Huilin Wang; Liubin Feng; Geoffrey I Webb; Lukasz Kurgan; Jiangning Song; Donghai Lin
- Source:
- Briefings in bioinformatics 2017 v.19 no.5 pp. 838-852
- ISSN:
- 1477-4054
- Subject:
- X-ray diffraction; algorithms; amino acid sequences; bioinformatics; crystallization; crystals; models; prediction; prioritization; proteins; structural genomics
- Abstract:
- ... X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-through ...
- DOI:
- 10.1093/bib/bbx018
- PubMed:
- 28334201
- PubMed Central:
- PMC6171492
- https://doi.org/10.1093/bib/bbx018
- Author:
- Wook Lee; Byungkyu Park; Daesik Choi; Kyungsook Han
- Source:
- Data in Brief 2017 v.10 pp. 561-563
- ISSN:
- 2352-3409
- Subject:
- RNA; amino acid sequences; data collection; nucleotide sequences; prediction; protein binding
- Abstract:
- ... Despite the increasing number of protein-RNA complexes in structure databases, few data resources have been made available which can be readily used in developing or testing a method for predicting either protein-binding sites in RNA sequences or RNA-binding sites in protein sequences. The problem of predicting protein-binding sites in RNA has received much less attention than the problem of predi ...
- DOI:
- 10.1016/j.dib.2016.12.041
- https://doi.org/10.1016/j.dib.2016.12.041
- Author:
- Ahmed Arslan; Vera van Noort
- Source:
- Bioinformatics 2017 v.33 no.2 pp. 151-154
- ISSN:
- 1460-2059
- Subject:
- DNA damage; Ebolavirus; amino acid sequences; bioinformatics; enzymes; evolution; germplasm conservation; humans; models; post-translational modification; prediction; protein-protein interactions; therapeutics; viral proteins; viruses
- Abstract:
- ... Motivation: The recent outbreak of Ebola virus disease (EVD) resulted in a large number of human deaths. Due to this devastation, the Ebola virus has attracted renewed interest as model for virus evolution. Recent literature on Ebola virus (EBOV) has contributed substantially to our understanding of the underlying genetics and its scope with reference to the 2014 outbreak. But no study yet, has fo ...
- DOI:
- 10.1093/bioinformatics/btw610
- PubMed:
- 27659453
- PubMed Central:
- PMC5942362
- https://doi.org/10.1093/bioinformatics/btw610
- Author:
- Xiao-Zhang Yu; Yu-Juan Lin; Chun-Jiao Lu; Xue-Hong Zhang
- Source:
- Ecotoxicology 2017 v.26 no.7 pp. 956-965
- ISSN:
- 0963-9292
- Subject:
- Arabidopsis; amino acid sequences; cysteine; cysteine synthase; gene expression regulation; genes; nitrilase; phylogeny; plant tissues; potassium cyanide; prediction; reverse transcriptase polymerase chain reaction; rice; roots; seedlings; shoots; transcription (genetics)
- Abstract:
- ... Involvement of genes (CYS-A1, CYS-C1 and NIT4) encoded with cysteine synthase, β-cyanoalanine synthase, nitrilase and cyanide metabolisms are evident in Arabidopsis. In the present study, identifications of CYS-A1, CYS-C1 and NIT4, predictions of conserved motifs, and constructions of phylogenetic relationships, based on their amino acid sequences in rice, were conducted. In order to elucidate the ...
- DOI:
- 10.1007/s10646-017-1824-1
- https://doi.org/10.1007/s10646-017-1824-1
- Author:
- Yogesh E. Thorat; S. Banerjee; Anil Kumar; B. Manimaran; P.K. Jain; Pankaj; Anil Sirohi
- Source:
- Indian journal of nematology 2017 v.47 no.1 pp. 121-126
- ISSN:
- 0974-4444
- Subject:
- Caenorhabditis elegans; Meloidogyne incognita; amino acid sequences; amino acids; bioinformatics; chromatin; computer simulation; essential genes; genomics; integrases; metabolism; nematology; phylogeny; prediction; root-knot nematodes; transcriptomics
- Abstract:
- ... The nematode house-keeping genes play a key role in basic functions of nematode metabolism and development. Although substantial research on house-keeping genes has been carried out in Caenorhabditis elegans, but their genomics and transcriptomics studies in plant-parasitic nematodes (PPNs) are limited. In the present investigation, a house-keeping Integrase gene from the southern root-knot nemato ...
- Author:
- Suresh Susan Aishwarya; Sellamuthu Iyappan; Kamepali Vijaya Lakshmi; Kandathil Narayanan Rajnish
- Source:
- 3 Biotech 2017 v.7 no.5 pp. 348
- ISSN:
- 2190-572X
- Subject:
- Chrysanthemum; Erwinia; Escherichia coli; Homo sapiens; Lactobacillus reuteri; amino acid sequences; asparaginase; asparagine; chromatography; gene expression; genes; isoelectric point; models; molecular cloning; molecular weight; open reading frames; pH; polyacrylamide gel electrophoresis; prediction; recombinant proteins; sequence alignment; sequence homology; substrate specificity; temperature; thermal stability
- Abstract:
- ... L-Asparaginase is employed in leukaemic treatment and in processing starchy foods. The in silico analysis of Lactobacillus reuteri DSM 20016 reveals the presence of an L-asparaginase gene with theoretical pI value of 4.99. 3D structure prediction was carried out and one model was selected based on the validation scores of 86.293 for ERRAT, 92.10% for VERIFY 3D and Ramachandran plot. Multiple seque ...
- DOI:
- 10.1007/s13205-017-0974-4
- PubMed:
- 28955645
- PubMed Central:
- PMC5612876
- https://doi.org/10.1007/s13205-017-0974-4
- Author:
- Sagar Banerjee; Sarvajeet Singh Gill; Pradeep Kumar Jain; Anil Sirohi
- Source:
- 3 Biotech 2017 v.7 no.1 pp. 64
- ISSN:
- 2190-572X
- Subject:
- Caenorhabditis elegans; Meloidogyne incognita; adults; amino acid sequences; collagen; complementary DNA; cysteine; egg masses; females; genes; models; molecular cloning; open reading frames; phylogeny; prediction; root-knot nematodes; sequence analysis
- Abstract:
- ... Cuticle collagens form a major part of the nematode cuticle and are responsible for maintaining the overall shape of the animal and its protection from the external environment. Although substantial research on cuticle collagen genes has been carried out in Caenorhabditis elegans, their isolation and characterization in plant parasitic nematodes have been limited to a few genes only. In this study ...
- DOI:
- 10.1007/s13205-017-0665-1
- PubMed:
- 28452012
- PubMed Central:
- PMC5428120
- https://doi.org/10.1007/s13205-017-0665-1
- Author:
- Li Huang; Xianhong Li; Pengfei Guo; Yuhua Yao; Bo Liao; Weiwei Zhang; Fayou Wang; Jiasheng Yang; Yulong Zhao; Hailiang Sun; Pingan He; Jialiang Yang
- Source:
- Bioinformatics 2017 v.33 no.20 pp. 3195-3201
- ISSN:
- 1460-2059
- Subject:
- Orthomyxoviridae; algorithms; amino acid sequences; antigenic variation; bioinformatics; computer software; epitopes; evolution; genetic variance; hemagglutination; hemagglutinins; immunologic techniques; influenza; influenza vaccines; models; prediction; sequence homology; vaccine development; viruses
- Abstract:
- ... Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completio ...
- DOI:
- 10.1093/bioinformatics/btx390
- https://doi.org/10.1093/bioinformatics/btx390
- Author:
- Lella Muralikrishna; Mahalakshmi Radhakrishnan
- Source:
- Biochemistry 2017 v.56 no.24 pp. 2971-2984
- ISSN:
- 1520-4995
- Subject:
- amino acid sequences; amino acids; membrane proteins; prediction
- Abstract:
- ... Every amino acid exhibits a different propensity for distinct structural conformations. Hence, decoding how the primary amino acid sequence undergoes the transition to a defined secondary structure and its final three-dimensional fold is presently considered predictable with reasonable certainty. However, protein sequences that defy the first principles of secondary structure prediction (they atta ...
- DOI:
- 10.1021/acs.biochem.7b00375
- https://doi.org/10.1021/acs.biochem.7b00375
- Author:
- Marco Necci; Damiano Piovesan; Zsuzsanna Dosztányi; Silvio C.E. Tosatto
- Source:
- Bioinformatics 2017 v.33 no.9 pp. 1402-1404
- ISSN:
- 1460-2059
- Subject:
- amino acid sequences; bioinformatics; databases; prediction; proteins; proteome
- Abstract:
- ... Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-base ...
- DOI:
- 10.1093/bioinformatics/btx015
- https://doi.org/10.1093/bioinformatics/btx015
- Author:
- Benjamin Lemaire; Sibel I. Karchner; Jared V. Goldstone; David C. Lamb; Jeffrey C. Drazen; Jean François Rees; Mark E. Hahn; John J. Stegeman
- Source:
- BBA - Proteins and Proteomics 2017 pp. -
- ISSN:
- 1570-9639
- Subject:
- Coryphaenoides armatus; amino acid sequences; amino acid substitution; catalytic activity; cytochrome P-450; cytosol; extremophiles; functional properties; glycosylation; high pressure treatment; hydrophilicity; hydrophobicity; ligands; lipid bilayers; marine fish; models; polypeptides; prediction; protein-protein interactions; proteomics; spectral analysis
- Abstract:
- ... Limited knowledge of the molecular evolution of deep-sea fish proteomes so far suggests that a few widespread residue substitutions in cytosolic proteins binding hydrophilic ligands contribute to resistance to the effects of high hydrostatic pressure (HP). Structure-function studies with additional protein systems, including membrane bound proteins, are essential to provide a more general picture ...
- DOI:
- 10.1016/j.bbapap.2017.06.026
- PubMed:
- 28694077
- PubMed Central:
- PMC5693637
- https://doi.org/10.1016/j.bbapap.2017.06.026
- Author:
- Chevonne E. Carlow; J. Trent Faultless; Christine Lee; Mahbuba Siddiqua; Alison Edge; Annette Nassuth
- Source:
- Plant physiology and biochemistry 2017 v.118 pp. 306-319
- ISSN:
- 0981-9428
- Subject:
- Arabidopsis; Vitis; amino acid sequences; amino acids; frost; hydrophobicity; models; molecular cloning; overwintering; phylogeny; plant response; prediction; promoter regions; sequence analysis; temperature; transcription (genetics); transcription factors; transcriptional activation; woody plants
- Abstract:
- ... The highly conserved CBF pathway is crucial in the regulation of plant responses to low temperatures. Extensive analysis of Arabidopsis CBF proteins revealed that their functions rely on several conserved amino acid domains although the exact function of each domain is disputed. The question was what functions similar domains have in CBFs from other, overwintering woody plants such as Vitis, which ...
- DOI:
- 10.1016/j.plaphy.2017.06.027
- https://doi.org/10.1016/j.plaphy.2017.06.027
- Author:
- Teerasak E-kobon; Ratiporn Leeanan; Saengtian Pannoi; Pornchai Anuntasomboon; Pacharee Thongkamkoon; Arinthip Thamchaipenet
- Source:
- BMC veterinary research 2017 v.13 no.1 pp. 243
- ISSN:
- 1746-6148
- Subject:
- Gram-negative bacteria; Pasteurella multocida; amino acid sequences; bioinformatics; buffaloes; cattle; genes; monitoring; oligopeptides; phylogeny; pneumonic pasteurellosis; polymerase chain reaction; prediction; screening; septicemia; subunit vaccines; surface proteins; swine; virulence; Thailand
- Abstract:
- ... BACKGROUND: Pasteurella multocida is a Gram-negative bacterium that causes economically significant infections of a broad range of animal species. Pneumonic and septicaemic pasteurellosis caused by this bacterium remain important problems in pigs, cattle, and water buffaloes in Thailand. The aim of this study was to characterise the virulence-associated gene profiles and to develop an OmpA molecul ...
- DOI:
- 10.1186/s12917-017-1157-6
- PubMed:
- 28814302
- PubMed Central:
- PMC5559837
- https://doi.org/10.1186/s12917-017-1157-6
- Author:
- Ralph Patrick; Bostjan Kobe; Kim-Anh Lê Cao; Mikael Bodén
- Source:
- Bioinformatics 2017 v.33 no.12 pp. 1773-1781
- ISSN:
- 1460-2059
- Subject:
- Internet; amino acid sequences; amino acids; bioinformatics; data collection; enzymes; genome-wide association study; prediction; protein phosphorylation; proteins; proteome
- Abstract:
- ... Motivation: Genome-wide association studies are identifying single nucleotide variants (SNVs) linked to various diseases, however the functional effect caused by these variants is often unknown. One potential functional effect, the loss or gain of protein phosphorylation sites, can be induced through variations in key amino acids that disrupt or introduce valid kinase binding patterns. Current met ...
- DOI:
- 10.1093/bioinformatics/btx072
- https://doi.org/10.1093/bioinformatics/btx072
- Author:
- Mittal Shriyaa; Shukla Diwakar
- Source:
- Journal of physical chemistry 2017 v.121 no.42 pp. 9761-9770
- ISSN:
- 1520-6106
- Subject:
- adrenergic receptors; amino acid sequences; calmodulin; electron paramagnetic resonance spectroscopy; models; molecular dynamics; peptide transporters; prediction
- Abstract:
- ... Double electron–electron resonance (DEER) spectroscopy is a powerful experimental technique for understanding the conformational heterogeneity of proteins. It involves attaching nitroxide spin labels to two residues in the protein to obtain a distance distribution between them. However, the choice of residue pairs to label in the protein requires careful thought, as experimentalists must pick labe ...
- DOI:
- 10.1021/acs.jpcb.7b04785
- https://doi.org/10.1021/acs.jpcb.7b04785
- Author:
- Dukka B KC
- Source:
- Briefings in bioinformatics 2017 v.18 no.6 pp. 1021-1032
- ISSN:
- 1477-4054
- Subject:
- amino acid sequences; computational methodology; models; prediction; proteins; structural biology
- Abstract:
- ... The most accurate characterizations of the structure of proteins are provided by structural biology experiments. However, because of the high cost and labor-intensive nature of the structural experiments, the gap between the number of protein sequences and solved structures is widening rapidly. Development of computational methods to accurately model protein structures from sequences is becoming i ...
- DOI:
- 10.1093/bib/bbw070
- https://doi.org/10.1093/bib/bbw070
- Author:
- Jan Zaucha; Jonathan G. Heddle
- Source:
- Computational and Structural Biotechnology Journal 2017 v.15 pp. 351-358
- ISSN:
- 2001-0370
- Subject:
- amino acid sequences; evolution; genetic drift; prediction; proteins
- Abstract:
- ... Biological molecules, like organisms themselves, are subject to genetic drift and may even become “extinct”. Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the seque ...
- DOI:
- 10.1016/j.csbj.2017.05.002
- PubMed:
- 28652896
- PubMed Central:
- PMC5472138
- https://doi.org/10.1016/j.csbj.2017.05.002
- Author:
- Jian Zhang; Lukasz Kurgan
- Source:
- Briefings in bioinformatics 2017 v.19 no.5 pp. 821-837
- ISSN:
- 1477-4054
- Subject:
- DNA; RNA; amino acid sequences; data collection; ligands; models; prediction; protein binding; protein-protein interactions
- Abstract:
- ... Understanding of molecular mechanisms that govern protein–protein interactions and accurate modeling of protein–protein docking rely on accurate identification and prediction of protein-binding partners and protein-binding residues. We review over 40 methods that predict protein–protein interactions from protein sequences including methods that predict interacting protein pairs, protein-binding re ...
- DOI:
- 10.1093/bib/bbx022
- https://doi.org/10.1093/bib/bbx022
- Author:
- Qingzhen Hou; Paul F. G. De Geest; Wim F. Vranken; Jaap Heringa; K. Anton Feenstra
- Source:
- Bioinformatics 2017 v.33 no.10 pp. 1479-1487
- ISSN:
- 1460-2059
- Subject:
- algorithms; amino acid sequences; amino acids; artificial intelligence; bioinformatics; data collection; prediction; protein-protein interactions; sequence analysis
- Abstract:
- ... Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in protein–protein ...
- DOI:
- 10.1093/bioinformatics/btx005
- https://doi.org/10.1093/bioinformatics/btx005
- Author:
- Meng-Si Li; Ting Li; Xue Lu; Le-Chang Sun; Yu-Lei Chen; Hong Liu; Min-Jie Cao; Guang-Ming Liu
- Source:
- Biochemical engineering journal 2017 v.125 pp. 196-205
- ISSN:
- 1369-703X
- Subject:
- thermal stability; heat inactivation; prediction; trypsin; Komagataella pastoris; sequence alignment; Carassius; site-directed mutagenesis; skeletal muscle; amino acid sequences; mutants; fish; Gibbs free energy; mass spectrometry; computer software; circular dichroism spectroscopy; half life
- Abstract:
- ... The myofibril-bound serine proteinase (MBSP) from the skeletal muscle of fish belongs to a class of trypsin-like serine proteinases with higher thermal stability than trypsin. To investigate the mechanism responsible for the thermal stability of MBSP from Crucian carp, mutagenesis of key residues were identified by amino acid sequence alignments and Protein Mutant Stability Prediction online predi ...
- DOI:
- 10.1016/j.bej.2017.06.007
- https://doi.org/10.1016/j.bej.2017.06.007
- Author:
- James B. Dale; Pierre R. Smeesters; Harry S. Courtney; Thomas A. Penfound; Claudia M. Hohn; Jeremy C. Smith; Jerome Y. Baudry
- Source:
- Vaccine 2017 v.35 no.1 pp. 19-26
- ISSN:
- 0264-410X
- Subject:
- amino acid sequences; antibacterial properties; antibodies; antiserum; bacteria; enzyme-linked immunosorbent assay; epitopes; hybrids; immune response; models; peptides; physicochemical properties; prediction; proteins; rabbits; recombinant vaccines
- Abstract:
- ... A major obstacle to the development of broadly protective M protein-based group A streptococcal (GAS) vaccines is the variability within the N-terminal epitopes that evoke potent bactericidal antibodies. The concept of M type-specific protective immune responses has recently been challenged based on the observation that multivalent M protein vaccines elicited cross-reactive bactericidal antibodies ...
- DOI:
- 10.1016/j.vaccine.2016.11.065
- PubMed:
- 27890396
- PubMed Central:
- PMC5143202
- https://doi.org/10.1016/j.vaccine.2016.11.065
- Author:
- Xiaolin Wu; Qinbin Zhang; Zhaokun Wu; Fuju Tai; Wei Wang
- Source:
- Briefings in bioinformatics 2017 v.19 no.6 pp. 1130-1140
- ISSN:
- 1477-4054
- Subject:
- Arabidopsis; amino acid sequences; apoplast; bioinformatics; cell walls; databases; experts; genomics; plant proteins; prediction; protein secretion; proteome; proteomics; rice; structural proteins; transcriptomics
- Abstract:
- ... The cell wall is the most striking feature that distinguishes plant cells from animal cells. It plays an essential role in cell shape, stability, growth and protection. Despite being present in small amounts, cell wall proteins (CWPs) are crucial components of the cell wall. The cell wall proteome generally consists of sensu stricto CWPs, apoplast proteins and extracellular secreted proteins. Curr ...
- DOI:
- 10.1093/bib/bbx050
- https://doi.org/10.1093/bib/bbx050
- Author:
- Pablo Mier; Miguel A Andrade-Navarro
- Source:
- Briefings in bioinformatics 2017 v.20 no.2 pp. 463-470
- ISSN:
- 1477-4054
- Subject:
- Archaea; amino acid sequences; bioinformatics; data collection; databases; models; prediction; proteins; proteome; sequence homology
- Abstract:
- ... Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromise ...
- DOI:
- 10.1093/bib/bbx127
- https://doi.org/10.1093/bib/bbx127
- Author:
- Heydar Maboudi Afkham; Xuanbin Qiu; Matthew The; Lukas Käll
- Source:
- Bioinformatics 2017 v.33 no.4 pp. 508-513
- ISSN:
- 1460-2059
- Subject:
- amino acid sequences; artificial intelligence; bioinformatics; computer software; liquid chromatography; models; peptides; prediction; proteomics; spectrometers; standard deviation; uncertainty
- Abstract:
- ... Motivation: Liquid chromatography is frequently used as a means to reduce the complexity of peptide-mixtures in shotgun proteomics. For such systems, the time when a peptide is released from a chromatography column and registered in the mass spectrometer is referred to as the peptide’s retention time. Using heuristics or machine learning techniques, previous studies have demonstrated that it is po ...
- DOI:
- 10.1093/bioinformatics/btw619
- https://doi.org/10.1093/bioinformatics/btw619