Genome-wide analysis of NAC transcription factors and their response to abiotic stress in celery (Apium graveolens L.).
This study provides a basis for the improved investigation of the structure and function of AgNAC TFs and celery stress resistance. PMID: 31809981 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - November 29, 2019 Category: Bioinformatics Authors: Duan AQ, Yang XL, Feng K, Liu JX, Xu ZS, Xiong AS Tags: Comput Biol Chem Source Type: research

Reporting a Transcript from Iranian Viola Tricolor, Which May Encode a Novel Cyclotide-Like Precursor: Molecular and in silico Studies.
In conclusion, using the cDNA screening method we found a potentially new cyclotide-like precursor gene and in silico studies revealed its significant characteristics that may open up a new research line on the distribution and evolution of cyclotides. PMID: 31791808 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - November 21, 2019 Category: Bioinformatics Authors: Khoshkam Z, Zarrabi M, Sepehrizadeh Z, Naghdi E, Aftabi Y Tags: Comput Biol Chem Source Type: research

Integrated analysis of the miRNA-mRNA next-generation sequencing data for finding their associations in different cancer types.
Abstract microRNAs (miRNAs) are short, non-coding, endogenous RNA molecule that regulates messenger RNAs (mRNAs) at the post-transcriptional level. The discovery of this regulatory relationship between miRNAs and mRNAs is an important research direction. In this regard, our method proposed an integrated approach to identify the mRNA targets of dysregulated miRNAs using next-generation sequencing data from six cancer types. For this analysis, a sensible combination of data mining tools is chosen. In particular, Random Forest, log-transformed Fold change, and Pearson correlation coefficient are considered to find th...
Source: Computational Biology and Chemistry - November 18, 2019 Category: Bioinformatics Authors: Bhowmick SS, Bhattacharjee D, Rato L Tags: Comput Biol Chem Source Type: research

Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen.
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 possibility of heterogeneous clinical observations of pharmacogenetic investigations is ignored. Above all, clinical investigation of all the polymorphic variants is beyond the scope of a pharmacogenetic study. Therefore, in order to understand the genotype-phenotype association, it is aimed to ...
Source: Computational Biology and Chemistry - November 17, 2019 Category: Bioinformatics Authors: Manish M, Lynn AM, Mishra S Tags: Comput Biol Chem Source Type: research

Proteome-wide analysis of protein disorder in Triticum aestivum and Hordeum vulgare.
n M Abstract There has been an increasing interest in Intrinsically Disordered Proteins (IDPs) ever since it was proven that they are ubiquitous and involved in key cellular functions. Interestingly, they have shown a large abundance in complete proteomes. In the current study, we have investigated the first large-scale study of the repertoire of IDPs in Triticum aestivum and Hordeum vulgare proteomes, in order to get insight into the biological roles of IDPs in both species. Results show that proteins in T. aestivum are significantly more disordered than those of H. vulgare. Moreover, the data revealed that DNA/R...
Source: Computational Biology and Chemistry - November 16, 2019 Category: Bioinformatics Authors: Choura M, Rebaï A, Hanin M Tags: Comput Biol Chem Source Type: research

In-silico therapeutic investigations of arjunic acid and arjungenin as an FXR agonist and validation in 3T3-L1 adipocytes.
Abstract The present study was to illustrate the agonistic property of arjungenin and arjunic acid towards farnesoid X receptor protein (FXR).The pharmacokinetic properties like molecular interactions, absorption, distribution, metabolism, elimination and toxicity (ADMET) of the ligands were checked through in-silico studies. Protein-ligand docking was carried out using autodock software. Molecular docking analysis confirmed strong binding energy and interaction of arjungenin and arjunic acid with the target protein and the ADMET profiles identified for both compounds were promising.Further in vitro studies were p...
Source: Computational Biology and Chemistry - November 15, 2019 Category: Bioinformatics Authors: T MM, T A, P BK, Fathima A, Khanum F Tags: Comput Biol Chem Source Type: research

Recent advances in computational modeling of fibrin clot formation: A review.
Abstract The field of thrombosis and hemostasis is crucial for understanding and developing new therapies for pathologies such as deep vein thrombosis, diabetes related strokes, pulmonary embolisms, and hemorrhaging related diseases. In the last two decades, an exponential growth in studies related to fibrin clot formation using computational tools has been observed. Despite this growth, the complete mechanism behind thrombus formation and hemostasis has been long and rife with obstacles; however, significant progress has been made in the present century. The computational models and methods used in this context a...
Source: Computational Biology and Chemistry - November 10, 2019 Category: Bioinformatics Authors: Yesudasan S, Averett RD Tags: Comput Biol Chem Source Type: research

Ligand based virtual screening using SVM on GPU.
Abstract In silico methods play an essential role in modern drug discovery methods. Virtual screening, an in silico method, is used to filter out the chemical space on which actual wet lab experiments are need to be conducted. Ligand based virtual screening is a computational strategy using which one can build a model of the target protein based on the knowledge of the ligands that bind successfully to the target. This model is then used to predict if the new molecule is likely to bind to the target. Support vector machine, a supervised learning algorithm used for classification, can be utilized for virtual screen...
Source: Computational Biology and Chemistry - November 10, 2019 Category: Bioinformatics Authors: Jayaraj PB, Jain S Tags: Comput Biol Chem Source Type: research

Taxonomy dimension reduction for colorectal cancer prediction.
In this study, we selected operational taxonomic units that include several kinds of microorganisms to predict colorectal cancer. To find the most important microorganisms and obtain the best prediction performance, we explore effective feature selection methods. We employ three main steps. First, we use a single method to reduce features. Next, to reduce the number of features, we integrate the dimension reduction methods correlation-based feature selection and maximum relevance-maximum distance (MRMD 1.0 and MRMD 2.0). Then, we selected the important features according to the taxonomy files. In this study, we created tra...
Source: Computational Biology and Chemistry - November 9, 2019 Category: Bioinformatics Authors: Qu K, Gao F, Guo F, Zou Q Tags: Comput Biol Chem Source Type: research

Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex.
Abstract The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 to form a ternary SnoN-SMAD3-SMAD4 complex in the TGFβ signaling pathway. However, how t...
Source: Computational Biology and Chemistry - November 9, 2019 Category: Bioinformatics Authors: Ji M, Ding Y, Li X, Mao N, Chen J Tags: Comput Biol Chem Source Type: research

Ant colony optimization for predicting RNA folding pathways.
Abstract RNA folding dynamics plays important roles in various functions of RNAs. To date, coarse-grained modeling has been successfully employed to simulate RNA folding dynamics on the energy landscape composed of secondary structures. In such a modeling, the energy barrier height between metastable structures is a key parameter that crucially affects the simulation results. Although a number of approaches ranging from the exact method to heuristic ones are available to predict the barrier heights, developing an efficient heuristic for this purpose is still an algorithmic challenge. We developed a novel RNA foldi...
Source: Computational Biology and Chemistry - November 4, 2019 Category: Bioinformatics Authors: Takitou S, Taneda A Tags: Comput Biol Chem Source Type: research

A deep learning ensemble for function prediction of hypothetical proteins from pathogenic bacterial species.
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, an...
Source: Computational Biology and Chemistry - October 19, 2019 Category: Bioinformatics Authors: Mishra S, Rastogi YP, Jabin S, Kaur P, Amir M, Khatun S Tags: Comput Biol Chem Source Type: research

PeSA: A software tool for peptide specificity analysis.
Abstract The discovery and characterization of molecular interactions is crucial towards a better understanding of complex biological processes. Particularly protein-protein interactions (i.e., PPIs), which are responsible for a variety of cellular functions from intracellular signaling to enzyme-substrate specificity, have been studied broadly over the past decades. Position-specific scoring matrices (PSSM) in particular are used extensively to help determine interaction specificity or candidate interaction motifs at the residue level. However, not all studies successfully report their results as a candidate inte...
Source: Computational Biology and Chemistry - October 17, 2019 Category: Bioinformatics Authors: Topcu E, Biggar KK Tags: Comput Biol Chem Source Type: research

Xanthine oxidase inhibitory activity of isoflavonoids from Apios americana.
Abstract Xanthine oxidase (XO) is a form of xanthine oxidoreductase, a type of enzyme that plays a key role in the induction of hyperuricemia and raising superoxide radical level in blood. The present study was performed to evaluate the inhibitory activity of isoflavonoids (1-3) isolated from the ethyl acetate fraction of Apios americana, on the catalytic reaction mediated by XO. The isoflavonoids exhibited potential inhibitory activity within microgram/mL along with quenching effect towards XO. A reduction in the respective IC50 values was observed in the presence of high concentration of substrate. Molecular doc...
Source: Computational Biology and Chemistry - October 5, 2019 Category: Bioinformatics Authors: Kim JH, Jin CH Tags: Comput Biol Chem Source Type: research

Pharmacoinformatics-based identification of anti-bacterial catalase-peroxidase enzyme inhibitors.
Abstract Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). In the present age, due to the rapid increase in antibiotic resistance worldwide, TB has become a major threat to human life. Regardless of significant efforts have been inclined to improve the healthcare systems for improving diagnosis, treatment, and anticipatory measures controlling TB is challenging. To date, there are no such therapeutic chemical agents available to fight or control the bacterial drug-resistance. The catalase-peroxidase enzyme (katG) which encoded by the katG gene of Mtb is most frequently getting ...
Source: Computational Biology and Chemistry - October 2, 2019 Category: Bioinformatics Authors: Jangam CS, Bhowmick S, Chorge RD, Bharatrao LD, Patil PC, Chikhale RV, AlFaris NA, ALTamimi JZ, Wabaidur SM, Islam MA Tags: Comput Biol Chem Source Type: research

Improved 3D-QSAR prediction by multiple-conformational alignment: A case study on PTP1B inhibitors.
Abstract Three-dimension quantitative structure activity relationship (3D-QSAR) was one of the major statistical techniques to investigate the correlation of biological activity with structural properties of candidate molecules, and the accuracy of statistic greatly depended on molecular alignment methodology. Exhaustive conformational search and successful conformational superposition could extremely improve the predictive accuracy of QSAR modeling. In this work, we proposed a solution to optimize QSAR prediction by multiple-conformational alignment methods, with a set of 40 flexible PTP1B inhibitors as case stud...
Source: Computational Biology and Chemistry - October 1, 2019 Category: Bioinformatics Authors: Zhang X, Mao J, Li W, Koike K, Wang J Tags: Comput Biol Chem Source Type: research

DistAA: Database of amino acid distances in proteins and web application for statistical review of distances.
Abstract Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interactions refers to geometric distances of amino acid pairs in polypeptide chains. For a detailed analysis of the amino acid distances, the database with three types of amino acid distances in a set of chains was created. Web application Distances of Amino Acids has also been developed to enable scientists to explore interactions of amino acids with different properties based on distances stored in the database. Web application calculates and displays descriptive stati...
Source: Computational Biology and Chemistry - September 28, 2019 Category: Bioinformatics Authors: Maljković MM Tags: Comput Biol Chem Source Type: research

Molecular determinants for ligand binding at Nav1.4 and Nav1.7 channels: Experimental affinity results analyzed by molecular modeling.
Abstract Here, we focused on exploring the selectivity mechanism against Nav1.7 over Nav1.4 due to different binding modes of two selected inhibitors. By the superposition of Nav1.7 and Nav1.4 proteins, we selected the most homologous chain of Nav1.7 with Nav1.4, defining the active site of Nav1.4-VSD4 based on the aryl sulfonamide binding site of Nav1.7-VSD4. Comparison of the conformations exhibited by Tyr1386 (Nav1.4) and Tyr1537 (Nav1.7) suggested that the steric hindrance caused by Tyr1386 owned primary influence on inhibition selectivity, which was further verified through molecular docking and MD simulation...
Source: Computational Biology and Chemistry - September 23, 2019 Category: Bioinformatics Authors: Kong DJ, Wang Y, Wang HX, Wang MX, Wang J, Cheng MS Tags: Comput Biol Chem Source Type: research

Kinetic flux vector splitting scheme for solving non-reactive multi-component flows.
Abstract This paper is about multi-component flow. There is no doubt that multi-component flow has a wide range of applications, specially in aerospace it plays a vital role during reentry of space ship into earth's atmosphere thats why it cannot be neglected for a proper vehicle design. In this paper one- and two-dimensional homogenous multi-component flow models are numerically investigated by using a high resolution splitting scheme and this scheme is known as Kinetic Flux Vector Splitting scheme. This scheme preserves positivity conditions and resolves shocks, rarefaction and contact discontinuity. The scheme ...
Source: Computational Biology and Chemistry - September 18, 2019 Category: Bioinformatics Authors: Saqib M, Rabbani A, Nisar UA, Ashraf W, Qamar S Tags: Comput Biol Chem Source Type: research

Target prediction of candidate miRNAs from Oryza sativa for silencing the RYMV genome.
Abstract In order to maintain a consistent supply of rice globally, control of pathogens affecting crop production is a matter of due concern. Rice yellow mottle virus(RYMV) is known to cause a variety of symptoms which can result in reduced yield. Four ORFs can be identified in the genome of RYMV encoding for P1 (ORF1), Polyprotein (processed to produce VPg, protease, helicase, RdRp4) (ORF2), putative RdRp (ORF3) and capsid/coat protein (ORF4). This research was aimed at identifying genome encoded miRNAs of O. sativa that are targeted to the genome of Rice Yellow Mottle Virus (RYMV). A consensus of four miRNA tar...
Source: Computational Biology and Chemistry - September 13, 2019 Category: Bioinformatics Authors: Jabbar B, Iqbal MS, Batcho AA, Nasir IA, Rashid B, Husnain T, Henry RJ Tags: Comput Biol Chem Source Type: research

Anticancer SAR establishment and novel accruing signal transduction model of drug action using biscoumarin scaffold.
Abstract In this paper, we have established methylenebis (4-hydroxy-2H-chromen-2-one) as a promising anticancer scaffold with kinesin spindle protein (KSP) inhibitory activity under malignant condition. A series of biscoumarin derivatives (MN1 to MN30) with different substituent were synthesized, and their anticancer activity was explored. Six biscoumarin derivatives that were found active were further selected to formulate organic nanoparticles (ONPs). Anticancer activity of both the forms (viz conventional and ONPs) was compared. MN30 was found most potent whereby MN10 showed good anticancer activity in both, i....
Source: Computational Biology and Chemistry - September 6, 2019 Category: Bioinformatics Authors: Mayank, Singh A, Kaur N, Garg N, Singh N Tags: Comput Biol Chem Source Type: research

Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods.
Abstract Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data. These data have different types (discrete, real, string, etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data (copy number variation, single nucleotide polymorphisms), annotations, interactions, and association data are some of the commonly used biological datasets to study various cellular mechanisms of living organisms. Each of them provides a unique, complementary and partly independ...
Source: Computational Biology and Chemistry - September 6, 2019 Category: Bioinformatics Authors: Wani N, Raza K Tags: Comput Biol Chem Source Type: research

Natural compounds as potential Hsp90 inhibitors for breast cancer-Pharmacophore guided molecular modelling studies.
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 function of numerous client proteins that are frequently upregulated and/or mutated in cancer cells, therefore, making Hsp90 inhibition a promising therapeutic strategy for the development of new efficacious drugs to treat breast cancer. In the present in silico investigation, a structure-base...
Source: Computational Biology and Chemistry - September 4, 2019 Category: Bioinformatics Authors: Rampogu S, Parate S, Parameswaran S, Park C, Baek A, Son M, Park Y, Park SJ, Lee KW Tags: Comput Biol Chem Source Type: research

Multi-targeted potential of Pittosporum senacia Putt.: HPLC-ESI-MSn analysis, in silico docking, DNA protection, antimicrobial, enzyme inhibition, anti-cancer and apoptotic activity.
gin G Abstract Pittosporum senacia (PS) Putt. (Pittosporaceae), indigenous to the Mascarene Islands, is a common ingredient in traditional medicines. However, there is currently a dearth of studies to validate some of these traditional claims. Given the broad traditional uses of PS against several diseases, we aimed to provide a comprehensive insight into the biological and chemical profile of P. senacia. The antioxidant, enzyme inhibitory activity, anticancer, and phytochemical composition of the methanolic extract of P. senacia leaf extracts were studied. The possible interaction and binding mode of the most abu...
Source: Computational Biology and Chemistry - August 29, 2019 Category: Bioinformatics Authors: Mahomoodally MF, Picot-Allain C, Hosenally M, Ugurlu A, Mollica A, Stefanucci A, Llorent-Martínez EJ, Baloglu MC, Zengin G Tags: Comput Biol Chem Source Type: research

Compositional features and codon usage pattern of TP63 gene.
Abstract The tumor protein p63encoded by the gene TP63 acts as a homologue of p53 protein. TP63 gene is the transformation factor with two initiation sites for transcriptional process and is related with stress, signal transduction and cell cycle control. The biasness in the preference of a few codons more frequently over other synonymous codons is the codon usage bias (CUB). Natural selection and mutational pressure are the two prime evolutionary forces acting on CUB. Here, the bioinformatic based analysis was performed to investigate the base distribution and CUB of TP63transcript variants (isoforms) as no work ...
Source: Computational Biology and Chemistry - August 28, 2019 Category: Bioinformatics Authors: Chakraborty S, Barbhuiya PA, Mazumder GA, Deb B, Uddin A Tags: Comput Biol Chem Source Type: research

In vitro antitumor activity, ADME-Tox and 3D-QSAR of synthesized and selected natural styryl lactones.
Abstract Prostate cancer is a common cause of death in men and a novel treating methods should be developed. In order to find a new drug for prostate cancer, a series of novel conformationally constrained analogues of (+)-goniofufurone and 7-epi-(+)-goniofufurone, as well as the newly synthesized styryl lactones containing the cinnamic acid ester groups were evaluated for in vitro cytotoxicity against prostate cancer cell (PC-3). Furthermore, prediction of physicochemical characteristics and drugability as well as in silico ADME-Tox tests of investigated compounds were performed. The 3D-QSAR model was established ...
Source: Computational Biology and Chemistry - August 23, 2019 Category: Bioinformatics Authors: Vukic VR, Loncar DM, Vukic DV, Jevric LR, Benedekovic G, Francuz J, Kojic V, Karadzic Banjac MZ, Popsavin V Tags: Comput Biol Chem Source Type: research

Biochemical and computational insights of adenosine deaminase inhibition by Epigallocatechin gallate.
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 development of anti-proliferative and anti-inflammatory drugs. In this work we studied adenosine deaminase inhibitory activity of epigallocatechin gallate by using biophysical and computational methods. The enzyme inhibition study result indicated that epigallocatechin gallate possess strong...
Source: Computational Biology and Chemistry - August 17, 2019 Category: Bioinformatics Authors: K G A, C S S, J A, C S Tags: Comput Biol Chem Source Type: research

Revelation of enzyme activity of mutant pyrazinamidases from Mycobacterium tuberculosis upon binding with various metals using quantum mechanical approach.
Abstract Pyrazinamide (PZA) is one of the most potent bacteriostatic drug against tuberculosis, a deadliest disease with high mortality and morbidity rate. PZA metabolizes into its active form pyrazinoic acid (POA) with the help of a metalloenzyme, pyrazinamidase (PZase). Mutagenicity and metal substitution in PZase weakens the binding of PZA with PZase and increases the drug resistance in Mycobacterium tuberculosis. The present study aims at the quantum mechanistic analysis of mutant-metal substituted PZase complexes by studying the mechanics of metals and PZA binding at MCS and catalytic site, respectively. A to...
Source: Computational Biology and Chemistry - August 16, 2019 Category: Bioinformatics Authors: Rasool N, Husssain W, Khan YD Tags: Comput Biol Chem Source Type: research

Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica.
Abstract Salmonella, an Enterobacteria is a therapeutically important pathogen for the host. The advancement of genome sequencing of S. enterica serovar Enteritidis have identified a distinct ROD9 pathogenic island, imparting virulence. The occurrence of 17 ROD9 hypothetical proteins, necessitates subsequent bioinformatics approach for structural and functional aspects of protein-protein relations or networks in different pathogenic phenotypes express. A collective analysis using predictive bioinformatics tools that includes NCBI-BLASTp and BLAST2GO annotated the motif patterns and functional significance. The VFD...
Source: Computational Biology and Chemistry - August 16, 2019 Category: Bioinformatics Authors: Soni N, Swain SK, Kant R, Singh A, Ravichandran R, Verma SK, Panda PK, Suar M Tags: Comput Biol Chem Source Type: research

Homology modeling and 3D-QSAR study of benzhydrylpiperazine δ opioid receptor agonists.
Homology modeling and 3D-QSAR study of benzhydrylpiperazine δ opioid receptor agonists. Comput Biol Chem. 2019 Aug 16;83:107109 Authors: Pan C, Meng H, Zhang S, Zuo Z, Shen Y, Wang L, Chang KJ Abstract The binding affinity of a series of benzhydrylpiperazine δ opioid receptor agonists were pooled and evaluated by using 3D-QSAR and homology modeling/molecular docking methods. Ligand-based CoMFA and CoMSIA 3D-QSAR analyses with 46 compounds were performed on benzhydrylpiperazine analogues by taking the most active compound BW373U86 as the template. The models were generated successfully with...
Source: Computational Biology and Chemistry - August 16, 2019 Category: Bioinformatics Authors: Pan C, Meng H, Zhang S, Zuo Z, Shen Y, Wang L, Chang KJ Tags: Comput Biol Chem Source Type: research

Influence of functional moiety in lupane-type triterpenoids in BACE1 inhibition.
Abstract Lupane-type triterpenoids have shown a potential effect against neurodegenerative disorders. Alzheimer's disease, one of the common neurodegenerative disease, is evident by the accumulation of amyloid-beta (Aβ) plaque in the extracellular regions of the brain. β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a key enzyme for the Aβ formation viathe cleavage of amyloid precursor protein (APP). Therefore, to find the potent BACE1 inhibitors and furthermore to explore the role of the functional group responsible for the strong BACE1 inhibitory activity, we synthesized a series of ...
Source: Computational Biology and Chemistry - August 14, 2019 Category: Bioinformatics Authors: Wagle A, Seong SH, Castro MJ, Faraoni MB, Murray AP, Jung HA, Choi JS Tags: Comput Biol Chem Source Type: research

Protein secondary structure prediction using neural networks and deep learning: A review.
Abstract Literature contains over fifty years of accumulated methods proposed by researchers for predicting the secondary structures of proteins in silico. A large part of this collection is comprised of artificial neural network-based approaches, a field of artificial intelligence and machine learning that is gaining increasing popularity in various application areas. The primary objective of this paper is to put together the summary of works that are important but sparse in time, to help new researchers have a clear view of the domain in a single place. An informative introduction to protein secondary structure ...
Source: Computational Biology and Chemistry - August 12, 2019 Category: Bioinformatics Authors: Wardah W, Khan MGM, Sharma A, Rashid MA Tags: Comput Biol Chem Source Type: research

TTAgP 1.0: A computational tool for the specific prediction of tumor T cell antigens.
, Farias JG Abstract Nowadays, cancer is considered a global pandemic and millions of people die every year because this disease remains a challenge for the world scientific community. Even with the efforts made to combat it, there is a growing need to discover and design new drugs and vaccines. Among these alternatives, antitumor peptides are a promising therapeutic solution to reduce the incidence of deaths caused by cancer. In the present study, we developed TTAgP, an accurate bioinformatic tool that uses the random forest algorithm for antitumor peptide predictions, which are presented in the context of MHC cl...
Source: Computational Biology and Chemistry - August 12, 2019 Category: Bioinformatics Authors: Beltrán Lissabet JF, Herrera Belén L, Farias JG Tags: Comput Biol Chem Source Type: research

Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations.
Abstract Shikimate dehydrogenase (SDH) catalyzes the reversible, NADPH-dependent reduction of 3-dehydroshikimate to shikimate, involved in the shikimate pathway. This pathway has emerged as an important target for the development of antimicrobial agent. Structural and functional analyses suggest that the conserved Lys69 plays an important role in the catalytic activity of Helicobacter pylori (H. pylori) SDH. However, the detailed mechanism how mutation of Lys69 affects the catalytic activity of H. pylori SDH remains unclear. Here, two-layered ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculation an...
Source: Computational Biology and Chemistry - August 9, 2019 Category: Bioinformatics Authors: Li J, Wu G, Fu Q, Ge H, Liu S, Li X, Cheng B Tags: Comput Biol Chem Source Type: research

Clumped-MCEM: Inference for multistep transcriptional processes.
Abstract Many biochemical events involve multistep reactions. Among them, an important biological process that involves multistep reaction is the transcriptional process. A widely used approach for simplifying multistep reactions is the delayed reaction method. In this work, we devise a model reduction strategy that represents several OFF states by a single state, accompanied by specifying a time delay for burst frequency. Using this model reduction, we develop Clumped-MCEM which enables simulation and parameter inference. We apply this method to time-series data of endogenous mouse glutaminase promoter, to valida...
Source: Computational Biology and Chemistry - August 1, 2019 Category: Bioinformatics Authors: Shetty KS, B A Tags: Comput Biol Chem Source Type: research

In silico and in vitro identification of candidate SIRT1 activators from Indonesian medicinal plants compounds database.
This study aimed to explore and identify medicinal plant compounds from Indonesian Herbal Database (HerbalDB) that might potentially become a candidate for SIRT1 activators through a combination of in silico and in vitro methods. Two pharmacophore models were developed using co-crystalized ligands that allosterically bind with SIRT1 similar to the putative ligands used by SIRT1 activators. Then, these were used for the virtual screening of HerbalDB. The identified compounds were subjected to molecular docking and 50 ns molecular dynamics simulation. Molecular dynamics simulation was analyzed using MM-GB(PB)SA methods. Th...
Source: Computational Biology and Chemistry - July 18, 2019 Category: Bioinformatics Authors: Azminah A, Erlina L, Radji M, Mun'im A, Syahdi RR, Yanuar A Tags: Comput Biol Chem Source Type: research

New SDC function prediction based on protein-protein interaction using bioinformatics tools.
ala J Abstract The precise roles for SDC have been complex to specify. Assigning and reanalyzing protein and peptide identification to novel protein functions is one of the most important challenges in postgenomic era. Here, we provide SDC molecular description to support, contextualize and reanalyze the corresponding protein-protein interaction (PPI). From SDC-1 data mining, we discuss the potential of bioinformatics tools to predict new biological rules of SDC. Using these methods, we have assembled new possibilities for SDC biology from PPI data, once, the understanding of biology complexity cannot be capture f...
Source: Computational Biology and Chemistry - July 16, 2019 Category: Bioinformatics Authors: Zandonadi FS, Castañeda Santa Cruz E, Korvala J Tags: Comput Biol Chem Source Type: research

Dynamics of human defensin 5 (HD5) self-assembly in solution: Molecular simulations/insights.
Abstract Human α -defensin 5 (HD5) is a 32-residue cysteine-rich host-defense peptide that exhibits broad-spectrum antimicrobial activity and plays an essential role in innate immunity in the human gut and other organ systems. Although its antimicrobial mechanism of action remains unclear, the high salt concentration seems to attenuate the antimicrobial function of HD5 via an unknown mechanism. In this work, we employ Molecular Dynamics (MD) simulations to analyse the oligomerization behaviour of HD5 when exposed to different salt concentration. We demonstrate that the presence of salt, such as sodium chlori...
Source: Computational Biology and Chemistry - July 13, 2019 Category: Bioinformatics Authors: Chairatana P, Niramitranon J, Pongprayoon P Tags: Comput Biol Chem Source Type: research

Disorder Atlas: Web-based software for the proteome-based interpretation of intrinsic disorder predictions.
Abstract Intrinsically disordered proteins lack a stable three-dimensional structure under physiological conditions. While this property has gained considerable interest within the past two decades, disorder poses substantial challenges to experimental characterization efforts. In effect, numerous computational tools have been developed to predict disorder from primary sequences, however, interpreting the output of these algorithms remains a challenge. To begin to bridge this gap, we present Disorder Atlas, web-based software that facilitates the interpretation of intrinsic disorder predictions using proteome-base...
Source: Computational Biology and Chemistry - July 13, 2019 Category: Bioinformatics Authors: Vincent M, Schnell S Tags: Comput Biol Chem Source Type: research

A comparison of classifiers for predicting the class color of fluorescent proteins.
Abstract Fluorescent proteins have been applied in a wide variety of fields ranging from basic science to industrial applications. Apart from the naturally occurring fluorescent proteins, there is a growing interest in genetically modified variants that emit light in a specific wavelength. Genetically modifying a protein is not an easy task, especially because the exchange of one residue by other has to achieve the desired property while maintaining protein stability. To help in the choice of residue exchange, computational methods are applied to predict function and stability of proteins. In this work we have pre...
Source: Computational Biology and Chemistry - July 9, 2019 Category: Bioinformatics Authors: da Silva RS, Marins LF, Almeida DV, Dos Santos Machado K, Werhli AV Tags: Comput Biol Chem Source Type: research

Meta-analysis of gene expression for development and validation of a diagnostic biomarker panel for Oral Squamous Cell Carcinoma.
Abstract We use a newly developed feature extraction and classification method to analyze previously published gene expression data sets in Oral Squamous Cell Carcinoma and in healthy oral mucosa in order to find a gene set sufficient for diagnoses. The feature selection technology is based on the relative dichotomy power concept published by us earlier. The resulting biomarker panel has 100% sensitivity and 95% specificity, is enriched in genes associated with oncogenesis and invasive tumor growth, and, unlike marker panels devised in earlier studies, shows concordance with previously published marker genes. ...
Source: Computational Biology and Chemistry - July 2, 2019 Category: Bioinformatics Authors: Makarov V, Gorlin A Tags: Comput Biol Chem Source Type: research

Maltase-glucoamylase inhibition potency and cytotoxicity of pyrimidine-fused compounds: An in silico and in vitro approach.
Abstract The prevalence of diabetes mellitus has been incremented in the current century and the need for novel therapeutic compounds to treat this disease has been significantly increased. One of the most promising approaches is to inhibit intestinal alpha glucosidases. Based on our previous studies, four pyrimidine-fused heterocycles (PFH) were selected as they revealed satisfactory inhibitory action against mammalian α-glucosidase. The interaction of these compounds with both active domains of human maltase-glucoamylase (MGAM) and their effect on human Caco-2 cell line were investigated. The docking asses...
Source: Computational Biology and Chemistry - June 19, 2019 Category: Bioinformatics Authors: Mehraban MH, Mansourian M, Ahrari S, HajiEbrahimi A, Odooli S, Motovali-Bashi M, Yousefi R, Ghasemi Y Tags: Comput Biol Chem Source Type: research

Insights into the flexibility of the T3 loop and GTPase activating protein (GAP) domain of dimeric α and β tubulins from a molecular dynamics perspective.
In this study, we explored the reasons for the flexibility and the rigidity of the β-α dimer and the α-β dimer respectively through molecular simulation and Anisotropic Normal Mode based analysis. As per the sequence alignment report, two glycine residues (Gly96 and Gly98) were observed in the T3 loop of the β subunit which get substituted by Asp98 and Ala100 in the T3 loop of the α subunit. The higher mobility of glycine residues contributes to the flexibility of the T3 loop of inter-dimer when they come in direct contact with the GTPase Activating Protein (GAP) domain of the subunit. This...
Source: Computational Biology and Chemistry - June 18, 2019 Category: Bioinformatics Authors: C SK, Gadewal N, Choudhary RK, Dasgupta D Tags: Comput Biol Chem Source Type: research

Structural, functional, and evolutionary analysis of late embryogenesis abundant proteins (LEA) in Triticum aestivum: A detailed molecular level biochemistry using in silico approach.
This study also demonstrated functional diversity in two class 6 proteins occurred due to many destabilizing mutations in the LEA4 domain that caused alteration of ligand binding and conformational shift from 310-helix → turn within the domain. The LEA4 domains of these proteins also showed functional similarity and evolutionary relatedness with three other proteins of genus Aegilops, denoting that these proteins in Triticum aestivum were derived from its ancestor Aegilops. The study also assigned LEApdB class 4 to an unclassified LEA protein 'WZY2-1' based on amino acid composition, conserved domain, motif architectu...
Source: Computational Biology and Chemistry - June 10, 2019 Category: Bioinformatics Authors: Bhattacharya S, Dhar S, Banerjee A, Ray S Tags: Comput Biol Chem Source Type: research

The architecture of the GhD7 promoter reveals the roles of GhD7 in growth, development and the abiotic stress response in rice.
This study was carried out to explore the transcription factor binding site (TFBS) architecture of the GhD7 promoter to identify the regulatory dynamics of GhD7 transcription. The promoter sequence (-2000 to +200 base pairs from the transcription start site) was retrieved from the PlantPAN 2.0 database. Ab initio promoter analysis, DNase I hypersensitive site (DHS) analysis, and methylation analysis were carried out to identify TFBSs. The TFBS diversity among rice varieties was also assessed. In addition to the previously identified 8 cis-elements, 448 novel cis-elements were identified in the GhD7 promoter that provide bi...
Source: Computational Biology and Chemistry - June 5, 2019 Category: Bioinformatics Authors: Herath V Tags: Comput Biol Chem Source Type: research

Genome-wide analysis of magnesium transporter genes in Solanum lycopersicum.
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 on their sequence homology. MGT genes are very diverse and possess very low sequence identity within its family. However, the Gly-Met-Asn (GMN) signature motif is present in most of the genes which are believed to be essential for Mg2+ recognition. In S. lycopersicum, different physiological root growth pattern was observed in both Mg excess and deficient conditions. Quantitative RT-PCR gene express...
Source: Computational Biology and Chemistry - May 30, 2019 Category: Bioinformatics Authors: Regon P, Chowra U, Awasthi JP, Borgohain P, Panda SK Tags: Comput Biol Chem Source Type: research

Structural prediction, whole exome sequencing and molecular dynamics simulation confirms p.G118D somatic mutation of PIK3CA as functionally important in breast cancer patients.
Abstract To understand the structural and functional importance of PIK3CA somatic mutations, whole exome sequencing, molecular dynamics simulation techniques in combination with in silico prediction algorithms such as SIFT, PolyPhen, Provean and CADD were employed. Twenty out of eighty missense somatic mutations in PIK3CA gene were found to be pathogenic by all the four algorithms. Most recurrent mutations found were known hotspot PIK3CA mutations with known clinical significance like p.E545 K, p.E545A, p.E545 G and p.C420R. A missense mutation p.G118D was found to be recurrently mutated in 5 cases. Interestin...
Source: Computational Biology and Chemistry - May 29, 2019 Category: Bioinformatics Authors: Masoodi TA, Shaik NA, Burhan S, Hasan Q, Shafi G, Talluri VR Tags: Comput Biol Chem Source Type: research

Alignment-independent 3D-QSAR and molecular docking studies of tacrine-4-oxo-4H-Chromene hybrids as anti-Alzheimer's agents.
Abstract A series of novel tacrine derivatives as multifunctional agents with potential inhibitory effects on both acetylcholinesterase(AChE) and butyrylcholinesterase (BuChE) enzymes for the treatment of Alzheimer's disease(AD), were applied to alignment independent 3D-QSAR methods using Pentacle software. In this studies, GRID-independent molecular descriptors (GRIND) analysis have been applied to characterize important interactions between enzymes and the studied compounds. Two H-bond acceptor groups as well as hydrophobic properties of tacrine rings for AChE and two H-bond acceptor on the carbonyl group of chr...
Source: Computational Biology and Chemistry - May 28, 2019 Category: Bioinformatics Authors: Manouchehrizadeh E, Mostoufi A, Tahanpesar E, Fereidoonnezhad M Tags: Comput Biol Chem Source Type: research

THPep: A machine learning-based approach for predicting tumor homing peptides.
Abstract In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agents. In this regard, the huge number of therapeutic peptides generated in recent years, demands the need to develop an effective and interpretable computational model for rapidly, effectively and automatically predicting tumor homing peptides. Therefore, a sequence-based approach referred herein as THPep has been developed to predict and analyze tumor homing pep...
Source: Computational Biology and Chemistry - May 24, 2019 Category: Bioinformatics Authors: Shoombuatong W, Schaduangrat N, Pratiwi R, Nantasenamat C Tags: Comput Biol Chem Source Type: research

Drug promiscuity: Exploring the polypharmacology potential of 1, 3, 6-trisubstituted 1, 4-diazepane-7-ones as an inhibitor of the 'god father' of immune checkpoint.
In this study, we utilized a drug repositioning approach to explore the characteristic feature of unrelated proteins to have similar binding sites and the promiscuity of drugs to repurpose an existing drug to target CTLA-4. CTLA-4 and Kallikrein-7 were found to have similar binding sites, we therefore used 1, 3, 6-trisubstituted 1, 4-diazepane-7-ones (TDSO) which is an inhibitor of Kallikrein-7 as our lead compound. High throughput screening using TDSO as a lead compound resulted in 9 hits with ZINC04515726 and ZINC08985213 having the highest binding score. We went ahead to investigate the interaction of these compounds wi...
Source: Computational Biology and Chemistry - May 22, 2019 Category: Bioinformatics Authors: Soremekun OS, Olotu FA, Agoni C, Soliman MES Tags: Comput Biol Chem Source Type: research