Theoretical ab initio study of the effects of methylation on structure and stability of G:C Watson-Crick base pair.

abstract：:Pertussis, caused by Bordetella pertussis is still one of the controversial diseases worldwide due to its high prevalence in both the developed and the developing countries, especially among young children. As currently approved vaccines are not protective enough and provide Th2-type immune responses, there is an urge...

journal_title：Journal of biomolecular structure & dynamics

authors： Souod N,Rismani E,Bahrami F,Pakzad SR,Ajdary S

更新日期：2020-07-21 00:00:00

abstract：:The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each...

journal_title：Journal of biomolecular structure & dynamics

authors： Haasnoot CA,Westerink HP,van der Marel GA,van Boom JH

更新日期：1984-10-01 00:00:00

abstract：:Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorptio...

journal_title：Journal of biomolecular structure & dynamics

authors： Roy A,Seal P,Sikdar J,Banerjee S,Haldar R

更新日期：2018-02-01 00:00:00

abstract：:We have developed an iterative hybrid algorithm (HA) to predict the 3D structure of peptides starting from their amino acid sequence. The HA is made of a modified genetic algorithm (GA) coupled to a local optimizer. Each HA iteration is carried out in two phases. In the first phase several GA runs are performed upon t...

journal_title：Journal of biomolecular structure & dynamics

authors： Garduño-Juárez R,Morales LB

更新日期：2003-08-01 00:00:00

abstract：:-1 programmed ribosomal frameshifting (PRF) in viruses is often stimulated by a pseudoknot downstream from the slippery sequence. At the PRF junction of HIV-1, transmissible gastroenteritis virus (TGEV), Barmah Forest virus (BFV), Fort Morgan virus (FMV), and Equine arteritis virus (EAV), we identified potential doubl...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang G,Yang Y,Huang X,Du Z

更新日期：2015-01-01 00:00:00

abstract：:We have analysed by various approaches the structure of cloned synthetic sequences in supercoiled plasmids. Individual inserts were formed by d(C-G)n blocks interrupted by the presence of A.T pairs positioned either in phase or out of phase of pur-pyr alternation. Based on the thermodynamic analysis we obtained result...

journal_title：Journal of biomolecular structure & dynamics

authors： Vlach J,Sponar J

更新日期：1990-04-01 00:00:00

abstract：:The unavailability of vaccine and medicines raised serious issues during COVID-19 pandemic and peoples from different parts of world relied on traditional medicine for their immediate recovery from COVID-19 and it found effective also. The current research aims to target COVID-19 immunological human host receptors i.e...

journal_title：Journal of biomolecular structure & dynamics

authors： Noor H,Ikram A,Rathinavel T,Kumarasamy S,Nasir Iqbal M,Bashir Z

更新日期：2021-01-25 00:00:00

abstract：:Malaria is still one of the deadly diseases resulting in deaths of millions of people worldwide and situation has become worse due to alarming rise in anti-malarial drug resistance. Genome sequence availability of Plasmodium falciparum, the main causal organism of severe malaria in humans, has enabled identification o...

journal_title：Journal of biomolecular structure & dynamics

authors： Kaushik A,Subramaniam S,Gupta D

更新日期：2014-01-01 00:00:00

abstract：:Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergenc...

journal_title：Journal of biomolecular structure & dynamics

authors： Costa Júnior DB,Araújo JSC,de Mattos Oliveira L,Neri FSM,Moreira POL,Taranto AG,Fonseca AL,de Pilla Varotti F,Leite FHA

更新日期：2020-05-13 00:00:00

abstract：:In recent years, acetylcholinesterase (AChE) and α-glycosidase (α-gly) inhibition have emerged as a promising and important approach for pharmacological intervention in many diseases such as glaucoma, epilepsy, obesity, cancer, and Alzheimer's. In this manner, the preparation and enzyme inhibition activities of periph...

journal_title：Journal of biomolecular structure & dynamics

authors： Koçyiğit ÜM,Taslimi P,Tüzün B,Yakan H,Muğlu H,Güzel E

更新日期：2020-12-09 00:00:00

abstract：:Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning-based AutoQSAR algorithm to generate drug leads for the flaviviruses-Dengue and West Nile. The drug leads generated by the program are fed as programmatic inputs to AutoDock Vina package for...

journal_title：Journal of biomolecular structure & dynamics

authors： Geoffrey B,Sanker A,Madaj R,Tresanco MSV,Upadhyay M,Gracia J

更新日期：2020-12-04 00:00:00

abstract：:Earlier identified strongest nucleosome DNA sequences of A. thaliana, those with visible 10-11 base sequence periodicity, are mapped along chromosomes. Resulting positional distributions reveal distinct maxima, one per chromosome, located in the centromere regions. Sequence-directed nucleosome mapping demonstrates tha...

journal_title：Journal of biomolecular structure & dynamics

authors： Salih B,Trifonov EN

更新日期：2015-01-01 00:00:00

abstract：:The binding of quinolones, nalidixic acid (Nal), oxolinic acid (Oxo) with double stranded polynucleotides was undertaken by using UV-melting, UV-Vis absorption, fluorescence and CD spectroscopic techniques. The binding of Nal or Oxo to the polynucleotides under low-salt buffer conditions were determined for poly (dA)....

journal_title：Journal of biomolecular structure & dynamics

authors： Jain A,Rajeswari MR

更新日期：2002-10-01 00:00:00

abstract：:The crystal-state preferred conformation of the terminally blocked hepta- and octapeptides with the general formula -(Aib)n L-Leu-(Aib)2- (n = 4 and 5, respectively), determined by X-ray diffraction, was found to be a right-handed 3(10)-helix stabilized by five and six consecutive intramolecular NH...O = C H-bonds of ...

journal_title：Journal of biomolecular structure & dynamics

authors： Bavoso A,Benedetti E,Di Blasio B,Pavone V,Pedone C,Toniolo C,Bonora GM,Formaggio F,Crisman M

更新日期：1988-02-01 00:00:00

abstract：:In order to investigate the interfacial activation of a lipase from Pseudomonas cepacia (PcL), molecular dynamics (MD) simulations and essential dynamics (ED) analysis were performed in different solvent environments: vacuum and explicit water solvents. Starting from the active (open) structure of PcL, the essential d...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee J,Suh SW,Shin S

更新日期：2000-10-01 00:00:00

abstract：:The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities...

journal_title：Journal of biomolecular structure & dynamics

authors： Haniford DB,Pulleyblank DE

更新日期：1983-12-01 00:00:00

abstract：:The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation...

journal_title：Journal of biomolecular structure & dynamics

authors： Pastor N,MacKerell AD Jr,Weinstein H

更新日期：1999-02-01 00:00:00

abstract：:We have carried out B3LYP hybrid density functional studies of complexes formed by cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine cytosine-tetrads with Li+, Na+ and K+ ions to determine their structures and interaction energies. The conformations studied have been restricted to a hydrogen bond pattern...

journal_title：Journal of biomolecular structure & dynamics

authors： Meyer M,Sühnel J

更新日期：2003-02-01 00:00:00

abstract：:Histone acetyltransferases (HATs) is one among the conspicuous posttranslational modification in eukaryotic cells. p300/CBP Associated Factor (PCAF) and CREB-binding protein (CBP) are the two highly homologous HAT family which are vastly implicated in several diseases like cancer, diabetes, etc. Pentadecylidenemalonat...

journal_title：Journal of biomolecular structure & dynamics

authors： Suryanarayanan V,Singh SK

更新日期：2019-06-01 00:00:00

abstract：:During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promo...

journal_title：Journal of biomolecular structure & dynamics

authors： Mitra S,Das P,Samadder A,Das S,Betai R,Chakrabarti J

更新日期：2015-01-01 00:00:00

abstract：:Thorough quantitative study of nucleosome repeat length (NRL) distributions, conducted in 1992 by J. Widom, resulted in a striking observation that the linker lengths between the nucleosomes are quantized. Comparison of the NRL average values with the MNase cut distances predicted from the hypothetical columnar struct...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2016-06-01 00:00:00

abstract：:A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy min...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Bhattacharyya D

更新日期：2013-01-01 00:00:00

abstract：:Donepezil is an acetylcholinesterase inhibitor (AChEI) in use to treat symptomatic patients of mild to moderate Alzheimer's disease (AD). Ferritin is an iron protein associated with storage and sequestration of excess ferrous iron in a way maintaining proper function of cellular processes and plays a key role in AD si...

journal_title：Journal of biomolecular structure & dynamics

authors： Shahwan M,Khan MS,Husain FM,Shamsi A

更新日期：2020-11-23 00:00:00

abstract：:Owing to its negative regulatory role in insulin signaling, protein tyrosine phosphatase of leukocyte antigen-related protein (PTP-LAR) was widely thought as a potential drug target for diabetes. Now, it was urgent to search for potential LAR inhibitors targeting diabetes. Initially, the pharmacophore models of LAR in...

journal_title：Journal of biomolecular structure & dynamics

authors： Du S,Yang B,Wang X,Li WY,Lu XH,Zheng ZH,Ma Y,Wang RL

更新日期：2020-09-01 00:00:00

abstract：:Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...

journal_title：Journal of biomolecular structure & dynamics

authors： Pan Z,Wang Y,Gu X,Wang J,Cheng M

更新日期：2020-10-01 00:00:00

abstract：:The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at...

journal_title：Journal of biomolecular structure & dynamics

authors： Razavi L,Raissi H,Hashemzadeh H,Farzad F

更新日期：2020-06-05 00:00:00

abstract：:We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role...

journal_title：Journal of biomolecular structure & dynamics

authors： Khechinashvili NN,Capital Ka Cyrillicabanov AV,Kondratyev MS,Polozov RV

更新日期：2014-01-01 00:00:00

abstract：:Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharmila DJ,Veluraja K

更新日期：2006-06-01 00:00:00

abstract：:Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...

journal_title：Journal of biomolecular structure & dynamics

authors： Wei Y,Yi Z,Xu J,Yang W,Yang L,Liu H

更新日期：2019-04-01 00:00:00

abstract：:Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

journal_title：Journal of biomolecular structure & dynamics

authors： Kashyap K,Kakkar R

更新日期：2020-01-01 00:00:00