Abstract:
:Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent of cost-effective and advanced sequencing techniques. To manage the pace of annotation with that of data generation, there is a shift to computational approaches which are based on homology, sequence and structure-based features, protein-protein interaction networks, phylogenetic profiles, and physicochemical properties, etc. A combination of these features has proven to be promising for protein function prediction in terms of improving prediction accuracy. In the present work, we have employed a combination of features based on sequence, physicochemical property, subsequence and annotation features with a total of 9890 features extracted and/or calculated for 171,212 reviewed prokaryotic proteins of 9 bacterial phyla from UniProtKB, to train a supervised deep learning ensemble model with the aim to categorize a bacterial hypothetical/unreviewed protein's function into 1739 GO terms as functional classes. The proposed system being fully dedicated to bacterial organisms is a novel attempt amongst various existing machine learning based protein function prediction systems based on mixed organisms. Experimental results demonstrate the success of the proposed deep learning ensemble model based on deep neural network method with F1 measure of 0.7912 on the prepared Test dataset 1 of reviewed proteins.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Mishra S,Rastogi YP,Jabin S,Kaur P,Amir M,Khatun Sdoi
10.1016/j.compbiolchem.2019.107147subject
Has Abstractpub_date
2019-12-01 00:00:00pages
107147eissn
1476-9271issn
1476-928Xpii
S1476-9271(19)30593-6journal_volume
83pub_type
杂志文章abstract::There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2012.12.003
更新日期:2013-04-01 00:00:00
abstract:BACKGROUND:Associating protein complexes to human inherited diseases is critical for better understanding of biological processes and functional mechanisms of the disease. Many protein complexes have been identified and functionally annotated by computational and purification methods so far, however, the particular rol...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.04.007
更新日期:2017-08-01 00:00:00
abstract::In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a librar...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2003.12.002
更新日期:2004-02-01 00:00:00
abstract::Interleukin-1β is a drug target in rheumatoid arthritis and several auto-immune disorders. In this study, a set of 48 compounds with the determined IC50 values were used for QSAR analysis by MOE. The QSAR model was developed by using training set of 41 compounds, based on 12 unique descriptors. Model was validated by ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.06.004
更新日期:2015-10-01 00:00:00
abstract::Microarray technology has been widely applied in study of measuring gene expression levels for thousands of genes simultaneously. Gene cluster analysis is found useful for discovering the function of gene because co-expressed genes are likely to share the same biological function. K-means is one of well-known clusteri...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.03.020
更新日期:2008-08-01 00:00:00
abstract::Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2006.01.001
更新日期:2006-04-01 00:00:00
abstract::Natural products as well as their derivatives play a significant role in the discovery of new biologically active compounds in the different areas of our life especially in the field of medicine. The synthesis of compounds produced from natural products including cytisine is one approach for the wider use of natural s...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107407
更新日期:2020-11-05 00:00:00
abstract::Proteins physically interact with each other and form protein complexes to perform their biological functions. The prediction of protein complexes from protein-protein interaction (PPI) network is usually difficult when the complexes are overlapping with each other in a dense region of the network. To address the prob...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.03.012
更新日期:2018-06-01 00:00:00
abstract::Our ability to detect differentially expressed genes in a microarray experiment can be hampered when the number of biological samples of interest is limited. In this situation, we propose the use of information from self-self hybridizations to acuminate our inference of differential expression. A unified modelling str...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.03.005
更新日期:2007-06-01 00:00:00
abstract::This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. ...
journal_title:Computational biology and chemistry
pub_type: 撤回出版物
doi:10.1016/j.compbiolchem.2016.02.010
更新日期:2016-02-17 00:00:00
abstract::Anethum sowa L. has been used as a spice herb in the Asian and European culinary systems to add flavour and taste. The studied plant has diverse folkloric medicinal value. Present study was designed to isolate phytochemicals from the hexane, chloroform and ethyl acetate extracts of the roots by various chromatographic...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.11.025
更新日期:2019-02-01 00:00:00
abstract::Zika virus (ZIKV) infection has been associated with Guillain-Barre syndrome in adults and microcephaly in infants. The existence of insufficient structural data in most of the protein databases hinders the synthesis of anti-ZIKV pharmaceutics. In this work, we attempted to model the catalytic domain of the ZIKV RNA p...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.10.007
更新日期:2017-12-01 00:00:00
abstract::Protein kinases are enzymes acting as a source of phosphate through ATP to regulate protein biological activities by phosphorylating groups of specific amino acids. For that reason, inhibiting protein kinases with an active small molecule plays a significant role in cancer treatment. To achieve this aim, computational...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107269
更新日期:2020-06-01 00:00:00
abstract::A computational inestigation on the difference in colors of two plants 'Peony' and 'Morning glory' by the same pigment 'Peonidin' has been performed by means of absorption characteristics. Peonidin imparts purple color to the flowers in Peony and blue to that in Morning glory. TDDFT tool in Gaussian 09 software packag...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.07.015
更新日期:2018-10-01 00:00:00
abstract::Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.03.005
更新日期:2018-06-01 00:00:00
abstract::Using wavelet packet decomposition, the energy coefficients in the fifth level of viral protein sequences were achieved to predict interspecies transmission. Since avian-origin influenza viruses could have high sequence similarities with human-origin avian influenza virus and could have the phenotype of interspecies t...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.11.029
更新日期:2019-02-01 00:00:00
abstract::Tissue softening accompanies the ripening of many fruits and initiates the processes of irreversible deterioration. Expansins are plant cell wall proteins that have been proposed to disrupt hydrogen bonds within the cell wall polymer matrix. Several authors have shown that FaEXPA2 is a key gene that shows an increased...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107279
更新日期:2020-05-30 00:00:00
abstract::DNA microarray data has been widely used in cancer research due to the significant advantage helped to successfully distinguish between tumor classes. However, typical gene expression data usually presents a high-dimensional imbalanced characteristic, which poses severe challenge for traditional machine learning metho...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.03.017
更新日期:2019-06-01 00:00:00
abstract::This paper describes an efficient algorithm based on a new concept called gene team for detecting conserved gene clusters among an arbitrary number of chromosomes. Within the clusters, neither the order of the genes nor their orientation need be conserved. In addition, insertion of foreign genes within the clusters ar...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s1476-9271(02)00097-x
更新日期:2003-02-01 00:00:00
abstract::The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107161
更新日期:2020-02-01 00:00:00
abstract::DNA interacts with small molecules, from water to endogenous reactive oxygen and nitrogen species, environmental mutagens and carcinogens, and pharmaceutical anticancer molecules. Understanding and predicting the physical interactions of small molecules with DNA via docking is key not only for the comprehension of mol...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.03.027
更新日期:2018-06-01 00:00:00
abstract::The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PT...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107123
更新日期:2019-12-01 00:00:00
abstract::The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we prop...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107327
更新日期:2020-10-01 00:00:00
abstract::An efficient, borax-catalyzed protocol for the synthesis of novel 4-aryl-substituted-4H-pyran derivatives fused to α-pyrone ring in a one-pot is described. By this achievement, some novel 4-aryl substituted 4H-pyrans fused to the α-pyrone ring as potential acetylcholinesterase inhibitors (AChEIs) with good to excellen...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.04.004
更新日期:2019-06-01 00:00:00
abstract::Glucokinase (GK) is the main enzyme which controls the blood glucose levels in a safe and narrow physiological range in humans. GK activators are the novel type of therapeutic agents which act on GK enzyme and show their anti-diabetic potential. The present work was planned to synthesize and evaluate the antidiabetic ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.02.018
更新日期:2018-04-01 00:00:00
abstract::Human intestinal absorption (HIA) of the drugs administered through the oral route constitutes an important criterion for the candidate molecules. The computational approach for predicting the HIA of molecules may potentiate the screening of new drugs. In this study, ensemble learning (EL) based qualitative and quanti...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.01.005
更新日期:2016-04-01 00:00:00
abstract::We have formulated the ab-initio prediction of the 3D-structure of proteins as a probabilistic programming problem where the inter-residue 3D-distances are treated as random variables. Lower and upper bounds for these random variables and the corresponding probabilities are estimated by nonparametric statistical metho...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s0097-8485(02)00074-8
更新日期:2003-07-01 00:00:00
abstract::It has recently been shown that cancer genes (oncogenes) tend to have heterogeneous expressions across disease samples. So it is reasonable to assume that in a microarray data only a subset of disease samples will be activated (often referred to as outliers), which presents some new challenges for statistical analysis...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.02.004
更新日期:2007-04-01 00:00:00
abstract::Proline is an important osmotic adjusting material greatly accumulated under drought stress and can help plant to adapt to osmotic stress. MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in plant development and stress response by negatively affecting gene expression at post-transcri...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2013.04.006
更新日期:2013-10-01 00:00:00
abstract::The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pneumonia etc. is becoming more difficult. Hence, it is crucial to unde...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.011
更新日期:2015-10-01 00:00:00