journal
MENU ▼
Read by QxMD icon Read
search

Computational Biology and Chemistry

journal
https://www.readbyqxmd.com/read/28826103/functional-contribution-of-coenzyme-specificity-determining-sites-of-7%C3%AE-hydroxysteroid-dehydrogenase-from-clostridium-absonum
#1
Deshuai Lou, Yue Wang, Jun Tan, Liancai Zhu, Shunlin Ji, Bochu Wang
Studies of the molecular determinants of coenzyme specificity help to reveal the structure-function relationship of enzymes, especially with regards to coenzyme specificity-determining sites (CSDSs) that usually mediate complex interactions. NADP(H)-dependent 7α-hydroxysteroid dehydrogenase from Clostridium absonum (CA 7α-HSDH), a member of the short-chain dehydrogenase/reductase superfamily (SDRs), possesses positively charged CSDSs that mainly contain T15, R16, R38, and R194, forming complicated polar interactions with the adenosine ribose C2 phosphate group of NADP(H)...
August 9, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28802167/induction-of-senescence-in-cancer-cells-by-5-aza-2-deoxycytidine-bioinformatics-and-experimental-insights-to-its-targets
#2
Jayarani F Putri, Nashi Widodo, Kazuichi Sakamoto, Sunil C Kaul, Renu Wadhwa
5'-Aza-2'-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy...
August 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28822333/virtual-screening-and-repositioning-of-inconclusive-molecules-of-beta-lactamase-bioassays-a-data-mining-approach
#3
Akshata Gad, Andrew Titus Manuel, Jinuraj K R, Lijo John, Sajeev R, Shanmuga Priya V G, Abdul Jaleel U C
This study focuses on the best possible way forward in utilizing inconclusive molecules of PubChem bioassays AID 1332, AID 434987 and AID 434955, which are related to beta-lactamase inhibitors of Mycobacterium tuberculosis (Mtb). The inadequacy in the experimental methods that were observed during the invitro screening resulted in an inconclusive dataset. This could be due to certain moieties present within the molecules. In order to reconsider such molecules, insilico methods can be suggested in place of invitro methods For instance, datamining and medicinal chemistry methods: have been adopted to prioritise the inconclusive dataset into active or inactive molecules...
July 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28780227/insights-into-the-immune-manipulation-mechanisms-of-pollen-allergens-by-protein-domain-profiling
#4
Seema Patel, Aruna Rani, Arun Goyal
Plant pollens are airborne allergens, as their inhalation causes immune activation, leading to rhinitis, conjunctivitis, sinusitis and oral allergy syndrome. A myriad of pollen proteins belonging to profilin, expansin, polygalacturonase, glucan endoglucosidase, pectin esterase, and lipid transfer protein class have been identified. In the present in silico study, the protein domains of fifteen pollen sequences were extracted from the UniProt database and submitted to the interactive web tool SMART (Simple Modular Architecture Research Tool), for finding the protein domain profiles...
July 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28803038/srsf-shape-analysis-for-sequencing-data-reveal-new-differentiating-patterns
#5
Sergiusz Wesolowski, Daniel Vera, Wei Wu
MOTIVATION: Sequencing-based methods to examine fundamental features of the genome, such as gene expression and chromatin structure, rely on inferences from the abundance and distribution of reads derived from Illumina sequencing. Drawing sound inferences from such experiments relies on appropriate mathematical methods to model the distribution of reads along the genome, which has been challenging due to the scale and nature of these data. RESULTS: We propose a new framework (SRSFseq) based on square root slope functions shape analysis to analyse Illumina sequencing data...
July 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28743101/in-silico-locating-the-immune-reactive-segments-of-lepidium-draba-peroxidase-and-designing-a-less-immune-reactive-enzyme-derivative
#6
Yaser Fattahian, Ali Riahi-Madvar, Reza Mirzaee, Gholamreza Asadikaram, Mohammad Reza Rahbar
Peroxidases have broad applications in industry, environmental as well as pharmaceutical and diagnosis. Recently applicability of peroxidases in cancer therapy was mentioned. In the present study, a horseradish peroxidase homologue from Lepidium draba was subjected to in silico analyzes aiming at identifying and locating immune-reactive regions. A derivative sequence with decreased immunogenicity and increased stability also suggested. The tertiary structure of the enzyme was predicted. The functional and structural importance of residues was annotated as well as the conservatory status of each residue...
July 17, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28735111/screening-disrupted-molecular-functions-and-pathways-associated-with-clear-cell-renal-cell-carcinoma-using-gibbs-sampling
#7
Ning Nan, Qi Chen, Yu Wang, Xu Zhai, Chuan-Ce Yang, Bin Cao, Tie Chong
OBJECTIVE: To explore the disturbed molecular functions and pathways in clear cell renal cell carcinoma (ccRCC) using Gibbs sampling. METHODS: Gene expression data of ccRCC samples and adjacent non-tumor renal tissues were recruited from public available database. Then, molecular functions of expression changed genes in ccRCC were classed to Gene Ontology (GO) project, and these molecular functions were converted into Markov chains. Markov chain Monte Carlo (MCMC) algorithm was implemented to perform posterior inference and identify probability distributions of molecular functions in Gibbs sampling...
July 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#8
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28797912/genome-wide-identification-functional-and-evolutionary-analysis-of-terpene-synthases-in-pineapple
#9
Xiaoe Chen, Wei Yang, Liqin Zhang, Xianmiao Wu, Tian Cheng, Guanglin Li
Terpene synthases (TPSs) are vital for the biosynthesis of active terpenoids, which have important physiological, ecological and medicinal value. Although terpenoids have been reported in pineapple (Ananas comosus), genome-wide investigations of the TPS genes responsible for pineapple terpenoid synthesis are still lacking. By integrating pineapple genome and proteome data, twenty-one putative terpene synthase genes were found in pineapple and divided into five subfamilies. Tandem duplication is the cause of TPS gene family duplication...
July 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28709136/tetracyclines-as-a-potential-antiviral-therapy-against-crimean-congo-hemorrhagic-fever-virus-docking-and-molecular-dynamic-studies
#10
Amirhossein Sharifi, Arash Amanlou, Faezeh Moosavi-Movahedi, Sahand Golestanian, Massoud Amanlou
Crimean-Congo Hemorrhagic Fever Virus (CCHFV) is one of the deadliest human diseases with mortality rate near 50%. Special attention should be paid to this virus since there is no approved treatment for it. On the other hand, the recent outbreak of Ebola virus which is a member of hemorrhagic fever viruses shows this group of viruses can be extremely dangerous. Previous studies have indicated that nucleoprotein of CCHFV, a pivotal protein in virus replication, is an appropriate target for antiviral drug development...
July 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28689108/multi-objective-feature-selection-for-warfarin-dose-prediction
#11
Mohammad Karim Sohrabi, Alireza Tajik
With increasing the application of decision support systems in various fields, using such systems in different aspects of medical science has been growing. Drug's dose prediction is one of the most important issues which can be improved using decision support systems. In this paper, a new multi-objective feature approach has been proposed to support warfarin dose prediction decision. Warfarin is an anticoagulant normally used in the prevention of the formation of clots. This research was conducted on 553 patients during 2013-2015 who were candidates for using warfarin and their INR was in the target range...
June 28, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28666141/computational-design-of-peptide-ligands-to-target-the-intermolecular-interaction-between-viral-envelope-protein-and-pediatric-receptor
#12
Darong Xu, Hongliang Bian, Jinlan Cai, Daocheng Bao, Qing Jin, Min Zhu, Cuifeng Zhang, Tingting Tao
The recognition and binding of viral envelope protein to pediatric receptor subverts the membrane-trafficking apparatus to mediate virion export in young children. Here, we described a successful computational design of peptide ligands to target the intermolecular interaction between the virus large envelope protein (LHB) and adaptin receptor (ADT). Based on the crystal structure of ADT in complex with an oligopeptide segment corresponding to the core binding site of LHB, a sequence-specific amino acid preference profile was determined systematically for the ADT-binding peptides using structural bioinformatics approach...
June 17, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28600956/differentiating-the-pre-hydrolysis-states-of-wild-type-and-a59g-mutant-hras-an-insight-through-md-simulations
#13
Neeru Sharma, Uddhavesh Sonavane, Rajendra Joshi
The most representative member of the Ras subfamily is its HRas isoform. Ras proteins being GTPases, possess an intrinsic activity to hydrolyze the GTP molecule to GDP. During the transition phases, between active and inactive states, P-loop and switch regions show maximum variations. Various hot-spot Ras mutants (G12V, A59G, Q61L etc) have been reported, that limit the protein's conformation in the permanent active state. In the present study, we aim to explore the structural dynamics of one such crucial mutant of Ras namely A59G which belongs to the conserved Switch II region of the protein...
June 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28599209/modelling-toxin-effects-on-protein-biosynthesis-in-eukaryotic-cells
#14
Vladas Skakauskas, Pranas Katauskis
We present a rather generic model for toxin (ricin) inhibition of protein biosynthesis in eukaryotic cells. We also study reduction of the ricin toxic effects with application of antibodies against the RTB subunit of ricin molecules. Both species initially are delivered extracellularly. The model accounts for the pinocytotic and receptor-mediated toxin endocytosis and the intact toxin exocytotic removal out of the cell. The model also includes the lysosomal toxin destruction, the intact toxin motion to the endoplasmic reticulum (ER) for separation of its molecules into the RTA and RTB subunits, and the RTA chain translocation into the cytosol...
May 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28587987/sphingosine-kinase-1-sk1-allosteric-inhibitors-that-target-the-dimerization-site
#15
Ozge Bayraktar, Elif Ozkirimli, Kutlu Ulgen
The sphingosine kinase 1 (SK1)/sphingosine-1-phosphate (S1P) signaling pathway is a crucial target for numerous human diseases from cancer to cardiovascular diseases. However, available SK1 inhibitors that target the active site suffer from poor potency, selectivity and pharmacokinetic properties. The selectivity issue of the kinases, which share a highly-conserved ATP-pocket, can be overcome by targeting the less-conserved allosteric sites. SK1 is known to function minimally as a dimer; however, the crystal structure of the SK1 dimer has not been determined...
May 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28587988/codon-usage-bias-and-its-influencing-factors-for-y-linked-genes-in-human
#16
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
The non-uniform usage of synonymous codons during translation of a protein is the codon usage bias and is mainly influenced by natural selection and mutation pressure. We have used bioinformatic approaches to analyze codon usage bias of human Y-linked genes. Effective number of codon (ENC) suggested that the overall extent of codon usage bias of genes was low. The relative synonymous codon usage (RSCU) analysis revealed that AGA and CTG codons were over-represented in Y-linked genes. Compositional constraint under mutation pressure influenced the codon usage pattern as revealed by the correspondence analysis (COA)...
May 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28601761/improving-virtual-screening-predictive-accuracy-of-human-kallikrein-5-inhibitors-using-machine-learning-models
#17
Xingang Fang, Sikha Bagui, Subhash Bagui
The readily available high throughput screening (HTS) data from the PubChem database provides an opportunity for mining of small molecules in a variety of biological systems using machine learning techniques. From the thousands of available molecular descriptors developed to encode useful chemical information representing the characteristics of molecules, descriptor selection is an essential step in building an optimal quantitative structural-activity relationship (QSAR) model. For the development of a systematic descriptor selection strategy, we need the understanding of the relationship between: (i) the descriptor selection; (ii) the choice of the machine learning model; and (iii) the characteristics of the target bio-molecule...
August 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28552695/identification-of-novel-human-renin-inhibitors-through-a-combined-approach-of-pharmacophore-modelling-molecular-dft-analysis-and-in-silico-screening
#18
Dhrubajyoti Gogoi, Vishwa Jyoti Baruah, Amrita Kashyap Chaliha, Bibhuti Bhushan Kakoti, Diganta Sarma, Alak Kumar Buragohain
Renin is an aspartyl protease of the renin-angiotensin system (RAS) and the first enzyme of the biochemical pathway for the generation of angiotensin II - a potent vasoconstrictor involved in the maintenance of cardiovascular homeostasis and the regulation of blood pressure. High enzymatic specificity of renin and its involvement in the catalysis of the rate-limiting step of the RAS hormone system qualify it as a good target for inhibition of hypertension and other associated diseases. Ligand-based pharmacophore model (Hypo1) was generated from a training set of 24 compounds with renin inhibitory activity...
August 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28575732/extra-precision-docking-free-energy-calculation-and-molecular-dynamics-studies-on-glutamic-acid-derivatives-as-murd-inhibitors
#19
Mohammed Afzal Azam, Srikanth Jupudi
The binding modes of well known MurD inhibitors have been studied using molecular docking and molecular dynamics (MD) simulations. The docking results of inhibitors 1-30 revealed similar mode of interaction with Escherichia coli-MurD. Further, residues Thr36, Arg37, His183, Lys319, Lys348, Thr321, Ser415 and Phe422 are found to be important for inhibitors and E. coli-MurD interactions. Our docking procedure precisely predicted crystallographic bound inhibitor 7 as evident from root mean square deviation (0...
May 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28570984/in-silico-identification-of-vaccine-candidates-against-klebsiella-oxytoca
#20
Sandipan Talukdar, Udeshna Bayan, Kandarpa Kr Saikia
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria...
May 22, 2017: Computational Biology and Chemistry
journal
journal
40315
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"