abstract：:MADS-box family transcription factors play key roles in various developmental processes in plants. Here, we identified 108 MADS-box genes in the genome of chrysanthemum (Chrysanthemum nankingense). We classified these genes based on their phylogenetic relationships with MADS-box genes in Arabidopsis thaliana and lettu...

journal_title：Computational biology and chemistry

authors： Won SY,Jung JA,Kim JS

更新日期：2020-12-05 00:00:00

abstract：:Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all...

journal_title：Computational biology and chemistry

authors： Mehmood A,Naseer S,Ali A,Fatimah H,Rehman S,Kiani AK

更新日期：2020-12-01 00:00:00

abstract：:MicroRNA (miRNA) plays an important role in life processes. In recent years, predicting the association between miRNAs and diseases has become a research hotspot. However, biological experiments take a lot of time and cost to identify pathogenic miRNAs. Computational biology-based methods can effectively improve accur...

journal_title：Computational biology and chemistry

authors： Ding Y,Jiang L,Tang J,Guo F

更新日期：2020-12-01 00:00:00

abstract：:With the development of cancer research, various gene expression datasets containing cancer information show an explosive growth trend. In addition, due to the continuous maturity of single-cell RNA sequencing (scRNA-seq) technology, the protein information and pedigree information of a single cell are also continuous...

journal_title：Computational biology and chemistry

authors： Ren LR,Gao YL,Liu JX,Zhu R,Kong XZ

更新日期：2020-12-01 00:00:00

abstract：:Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particul...

journal_title：Computational biology and chemistry

authors： Pitsillou E,Liang J,Karagiannis C,Ververis K,Darmawan KK,Ng K,Hung A,Karagiannis TC

更新日期：2020-12-01 00:00:00

abstract：:Accurate clustering of cells from single-cell RNA sequencing (scRNA-seq) data is an essential step for biological analysis such as putative cell type identification. However, scRNA-seq data has high dimension and high sparsity, which makes traditional clustering methods less effective to reflect the similarity between...

journal_title：Computational biology and chemistry

authors： Li J,Jiang W,Han H,Liu J,Liu B,Wang Y

更新日期：2020-11-18 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

authors： Metelytsia LO,Trush MM,Kovalishyn VV,Hodyna DM,Kachaeva MV,Brovarets VS,Pilyo SG,Sukhoveev VV,Tsyhankov SA,Blagodatnyi VM,Semenyuta IV

更新日期：2020-11-05 00:00:00

abstract：:Development in two-dimensional (2D) drug-delivery materials have quickly translated into biological and pharmacological fields. In this present work, pristine graphene (PG) and hexagonal boron nitride (h-BN) sheets are explored as a drug carrier for cytarabine (CYT) and clofarabine (CLF) anti-cancer drugs using densit...

journal_title：Computational biology and chemistry

authors： Saravanan V,Rajamani A,Subramani M,Ramasamy S

更新日期：2020-10-01 00:00:00

abstract：:The accurate prognostic prediction is essential for precise diagnosis and treatment of carcinoma. In addition to clinical survival prediction method, many computational methods based on transcriptomic data have been proposed to build the prediction models and study the prognosis of cancer patients. We propose a differ...

journal_title：Computational biology and chemistry

authors： Li J,Ping Y,Li H,Li H,Liu Y,Liu B,Wang Y

更新日期：2020-10-01 00:00:00

abstract：:Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina...

journal_title：Computational biology and chemistry

authors： Li J,Song Y,Li F,Zhang H,Liu W

更新日期：2020-10-01 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

authors： Luo F,Chen C,Fuentes J

更新日期：2020-10-01 00:00:00

abstract：:3CL proteases (3CLpro) are only found in RNA viruses and have a central role in polyprotein processing during replication. Therefore, 3CLpro has emerged as promising drug target for therapeutic treatment of infections caused by Coronaviruses. In the light of the recent major outbreak of the SARS-CoV-2 virus and the co...

journal_title：Computational biology and chemistry

authors： Meyer-Almes FJ

更新日期：2020-10-01 00:00:00

abstract：:In this work, a framework is provided for identifying intracranial electroencephalography (iEEG) seizures based on discrete wavelet transform (DWT) analysis of iEEG signals using forward propagation and feedback neural networks. The performance of 5 different data sets combination classifications is studied using the ...

journal_title：Computational biology and chemistry

authors： Gong C,Zhang X,Niu Y

更新日期：2020-06-19 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

authors： Arian R,Hariri A,Mehridehnavi A,Fassihi A,Ghasemi F

更新日期：2020-06-01 00:00:00

abstract：:We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xT...

journal_title：Computational biology and chemistry

authors： Alshammari N,Platts JA

更新日期：2020-06-01 00:00:00

abstract：:Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from ri...

journal_title：Computational biology and chemistry

authors： Hussain A,Shahbaz M,Tariq M,Ibrahim M,Hong X,Naeem F,Khalid Z,Raza HMZ,Bo Z,Bin L

更新日期：2020-06-01 00:00:00

abstract：:Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calcula...

journal_title：Computational biology and chemistry

authors： Sai Phani Kumar V,Verma M,Deshpande PA

更新日期：2020-06-01 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

authors： Valenzuela-Riffo F,Morales-Quintana L

更新日期：2020-05-30 00:00:00

abstract：:Currently Alzheimer's disease (AD) is a devastating neurological disorder that mainly affects the elderly. The treatment of AD has as main objective to increase the levels of ACh in the synaptic cleft by inhibiting the cholinesterase enzymes, which are responsible for the degradation of ACh. Twenty one synthesized cou...

journal_title：Computational biology and chemistry

authors： de Souza LG,Moraes PF,Leão RAC,Costa PRR,Soares RO,Pascutti PG,Figueroa-Villar JD,Rennó MN

更新日期：2020-05-29 00:00:00

abstract：:The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. The...

journal_title：Computational biology and chemistry

authors： Jin Z,Wang Y,Yu XF,Tan QQ,Liang SS,Li T,Zhang H,Shaw PC,Wang J,Hu C

更新日期：2020-04-01 00:00:00

abstract：BACKGROUND:Metastasis is the main cause of breast cancer (BC) lethality, especially in early stages, led to improvements in therapeutic procedures. Lately, by improvements in our perception of biological processes and immune system new classes of vaccines are emerged that grant us the opportunity of designing resolute ...

journal_title：Computational biology and chemistry

authors： Afzali F,Minuchehr Z,Jahangiri S,Ranjbar MM

更新日期：2020-04-01 00:00:00

abstract：:The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world,...

journal_title：Computational biology and chemistry

authors： Hattori LT,Gutoski M,Vargas Benítez CM,Nunes LF,Lopes HS

更新日期：2020-02-01 00:00:00

abstract：:A series of indole-derived methoxylated chalcones were described as anti-dermatophyte agents. The in vitro antifungal susceptibility testing against different dermatophytes revealed that most of compounds had potent activity against the dermatophyte strains. In particular, the 4-ethoxy derivative 4d with MIC values of...

journal_title：Computational biology and chemistry

authors： Mirzaei H,Abastabar M,Emami S

更新日期：2020-02-01 00:00:00

abstract：:Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...

journal_title：Computational biology and chemistry

authors： Manish M,Lynn AM,Mishra S

更新日期：2020-02-01 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

authors： Kovačević S,Banjac MK,Podunavac-Kuzmanović S,Milošević N,Ćurčić J,Vulić J,Šeregelj V,Banjac N,Ušćumlić G

更新日期：2020-02-01 00:00:00

abstract：:Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD+) in the subsequent steps. Leishmania protozoan parasites are NAD+ auxotrophs and need precursors (nicoti...

journal_title：Computational biology and chemistry

authors： Chauhan N,Poddar R

更新日期：2019-12-01 00:00:00

abstract：:Breast cancer is one of the major impediments affecting women globally. The ATP-dependant heat shock protein 90 (Hsp90) forms the central component of molecular chaperone machinery that predominantly governs the folding of newly synthesized peptides and their conformational maturation. It regulates the stability and f...

journal_title：Computational biology and chemistry

authors： Rampogu S,Parate S,Parameswaran S,Park C,Baek A,Son M,Park Y,Park SJ,Lee KW

更新日期：2019-12-01 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

authors： Sun YZ,Wu JW,Lu XH,Ma Y,Wang RL

更新日期：2019-12-01 00:00:00

abstract：:Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...

journal_title：Computational biology and chemistry

authors： Kong J,Li L,Zhimin L,Yan J,Ji D,Chen Y,Yuanyuan W,Chen X,Shao H,Wang J,Da Z

更新日期：2019-12-01 00:00:00

abstract：:Epigallocatechin gallate, a flavonoid from Camellia sinensis possess various pharmacological activities such as anticancer, antimicrobial and antioxidant etc. Adenosine deaminase, (ADA), is a key enzyme involved in the purine metabolism, the inhibitors of which is being considered as highly promising candidate for the...

journal_title：Computational biology and chemistry

authors： K G A,C S S,J A,C S

更新日期：2019-12-01 00:00:00

abstract：:The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions ...

journal_title：Computational biology and chemistry

authors： Mamet N,Harari G,Zamir A,Bachelet I

更新日期：2019-12-01 00:00:00

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 ...

journal_title：Computational biology and chemistry

authors： Mishra S,Rastogi YP,Jabin S,Kaur P,Amir M,Khatun S

更新日期：2019-12-01 00:00:00

abstract：:Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...

journal_title：Computational biology and chemistry

authors： Ghasemi RH,Keramati M,Mojarrad MHS

更新日期：2019-12-01 00:00:00

abstract：:The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...

journal_title：Computational biology and chemistry

authors： Raajaraman BR,Sheela NR,Muthu S

更新日期：2019-10-01 00:00:00

abstract：:A computational study of the interaction of cardiac troponin I (cTnI) with its specific antibody and of that antibody with skeletal troponin I (sTnI), the principal interferon of cTnI, is carried out. Computational and simulation tools such as FTSite, FTMap, FTDock and pyDock are used to determine the binding sites of...

journal_title：Computational biology and chemistry

authors： Sabek J,Martínez-Pérez P,García-Rupérez J

更新日期：2019-06-01 00:00:00

abstract：:Laminin-111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin-111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post - translational modificati...

journal_title：Computational biology and chemistry

authors： Galliou PA,Verrou KM,Koliakos G

更新日期：2019-06-01 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

authors： He Y,Zhou J,Lin Y,Zhu T

更新日期：2019-06-01 00:00:00

abstract：:Magnesium (Mg) is an important micronutrient for various physiological processes in plants. In this study, putative Magnesium Transporter (MGT) genes have been identified in Solanum lycopersicum, Solanum tuberosum, Brachypodium distachyon, Fagaria vesca, Brassica juncea and were classified into 5 distinct groups based...

journal_title：Computational biology and chemistry

authors： Regon P,Chowra U,Awasthi JP,Borgohain P,Panda SK

更新日期：2019-06-01 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

authors： Pourshojaei Y,Abiri A,Eskandari R,Dourandish F,Eskandari K,Asadipour A

更新日期：2019-06-01 00:00:00

abstract：BACKGROUND:Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment f...

journal_title：Computational biology and chemistry

authors： Buiga P,Elson A,Tabernero L,Schwartz JM

更新日期：2019-06-01 00:00:00