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You searched for: Publication year rev 7983-2017 Remove constraint Publication year rev: 7983-2017 Subject term amino acid sequences Remove constraint Subject term: amino acid sequences Subject term prediction Remove constraint Subject term: prediction Text availability Citation in PubAg Remove constraint Text availability: Citation in PubAg
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1. A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites

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

2. A study to evaluate the potential of an in silico approach for predicting dipeptidyl peptidase-IV inhibitory activity in vitro of protein hydrolysates

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

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

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

5. DeepLoc: prediction of protein subcellular localization using deep learning

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

6. Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity

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

7. FELLS: fast estimator of latent local structure

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

8. Feeding recombinant E. coli with GST-mBmKTX fusion protein increases the fecundity and lifespan of Caenorhabditis elegans

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

9. Genome wide analysis of NAC gene family ‘sequences’ in sugarcane and its comparative phylogenetic relationship with rice, sorghum, maize and Arabidopsis for prediction of stress associated NAC genes

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

10. Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features

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

11. ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model

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

12. Identification of the adenovirus type 2 C-168 protein

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

13. Infectious spleen and kidney necrosis disease (ISKND) outbreaks in farmed barramundi (Lates calcarifer) in Vietnam

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

14. MIToS.jl: mutual information tools for protein sequence analysis in the Julia language

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

15. Novel poly-uridine insertion in the 3′UTR and E2 amino acid substitutions in a low virulent classical swine fever virus

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

16. Protein binding hot spots prediction from sequence only by a new ensemble learning method

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

17. RBPPred: predicting RNA-binding proteins from sequence using SVM

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

18. Structural classification of proteins using texture descriptors extracted from the cellular automata image

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

19. 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

20. pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites

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

21. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC

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

22. 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

23. A sequence-based computational method for prediction of MoRFs

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

24. Antimicrobial effect of the 60S ribosomal protein L29 (cgRPL29), purified from the gill of pacific oyster, Crassostrea gigas

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

25. 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

26. Characterization of the DNA mismatch repair proteins MutS and MutL in a hypermutator Acinetobacter baumannii

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

27. 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

28. Data of protein-RNA binding sites

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

29. Identification and expression analysis of CYS-A1, CYS-C1, NIT4 genes in rice seedlings exposed to cyanide

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

30. In silico Analysis of Root-Knot Nematode, Meloidogyne incognita House-Keeping Gene

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 ...

31. Matrix completion with side information and its applications in predicting the antigenicity of influenza viruses

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

32. Metamorphic Proteins: Emergence of Dual Protein Folds from One Primary Sequence

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

33. MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins

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

34. Nuclear localization and transactivation by Vitis CBF transcription factors are regulated by combinations of conserved amino acid domains

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

35. PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

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

36. Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity

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

37. Recent advances in sequence-based protein structure prediction

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

38. Review and comparative assessment of sequence-based predictors of protein-binding residues

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

39. Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest

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

40. Site-directed mutagenesis of myofibril-bound serine proteinase from Crucian carp: possible role of Pro95, A127 and I130 on thermal stability

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

41. Subcellular locations of potential cell wall proteins in plants: predictors, databases and cross-referencing

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

42. Toward completion of the Earth’s proteome: an update a decade later

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

43. Uncertainty estimation of predictions of peptides’ chromatographic retention times in shotgun proteomics

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