Quantum-chemical analysis of C-H...O and C-H...N interactions in RNA base pairs--H-bond versus anti-H-bond pattern.

abstract：:Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. o...

journal_title：Journal of biomolecular structure & dynamics

authors： Lei Y,Kang SK,Gao J,Jia XS,Chen LL

更新日期：2013-03-01 00:00:00

abstract：:Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium...

journal_title：Journal of biomolecular structure & dynamics

authors： Desai PV,Avery MA

更新日期：2004-06-01 00:00:00

abstract：:Two naphthalene-containing compounds, 4-hydroxy-6,7-dimethoxy-1-(4-(trifluoromethyl)phenyl)-2-naphthoic acid (A) and 4-hydroxy-6,7-dimethoxy-1-phenyl-2-naphthoic acid (B), were prepared by several steps. Their bindings to human serum albumin (HSA) were studied by ultraviolet-visible (UV-vis) absorption, fluorescence, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang X,Xing Y,Su J,Wang C,Wang Z,Yu Y,Xu H,Ma D

更新日期：2020-06-12 00:00:00

abstract：:Melanoma is a malignant cancer of the skin associated with a high mortality. Early medical diagnosis and surgical intervention are essential for the treatment of melanoma. The use of plant-based compounds is an important strategy for the prevention and treatment of different types of cancers. Curcumin is a promising n...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghazaeian M,Khorsandi K,Hosseinzadeh R,Naderi A,Abrahamse H

更新日期：2020-08-07 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：:Minidumbbell (MDB) is a newly found non-B DNA structure formed by short single-strand sequences. Up to now, three MDBs have been reported to form at neutral pH by sequences containing two repeats of TTTA, CCTG and CTTG. Among them, the thermodynamically less stable TTTA and CCTG MDBs have been proposed to be the struc...

journal_title：Journal of biomolecular structure & dynamics

authors： Guo P,Lam SL

更新日期：2020-04-01 00:00:00

abstract：:The selective recognition of the aminoterminal binding pharmacophore Tyr-D-Xaa-Phe of the opioid heptapeptide dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2 (DRM)1, and of dermenkephalin, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2 (DREK), by the mu-opioid receptor and delta-opioid receptor, respectively, depends upon the consti...

journal_title：Journal of biomolecular structure & dynamics

authors： Riand J,Baron D,Nicolas P,Benajiba A,Teng Y,Naim M

更新日期：1999-12-01 00:00:00

abstract：:The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, a...

journal_title：Journal of biomolecular structure & dynamics

authors： Usha S,Selvaraj S

更新日期：2014-01-01 00:00:00

abstract：:Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials hav...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee SA,Pinnick DA,Anderson A

更新日期：2015-01-01 00:00:00

abstract：:Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen bonded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To ch...

journal_title：Journal of biomolecular structure & dynamics

authors： Kiran MR,Bansal M

更新日期：1998-12-01 00:00:00

abstract：:Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distributio...

journal_title：Journal of biomolecular structure & dynamics

authors： Beveridge DL,Maye PV,Jayaram B,Ravishanker G,Mezei M

更新日期：1984-10-01 00:00:00

abstract：:Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...

journal_title：Journal of biomolecular structure & dynamics

authors： Petrauskene OV,Yakovleva JN,Alekseev YI,Subach FV,Babkina OV,Gromova ES

更新日期：2000-04-01 00:00:00

abstract：:In the course of studies related to new molecules with intercalative properties, we have been led to design and synthesize a bithiazole derivative, namely the 2-phenyl-6-[2'-(4'-(ethoxy-carbonyl)thiazolyl)]thiazolo[3,2- b][1,2,4]triazole (PETT). Its interaction with calf thymus DNA was studied using thermal denaturati...

journal_title：Journal of biomolecular structure & dynamics

authors： Houssin R,Helbecque N,Bernier JL,Henichart JP

更新日期：1986-10-01 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：:For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in ...

journal_title：Journal of biomolecular structure & dynamics

authors： Rosandić M,Vlahović I,Glunčić M,Paar V

更新日期：2016-07-01 00:00:00

abstract：:The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial di...

journal_title：Journal of biomolecular structure & dynamics

authors： Uberbacher EC,Bunick GJ

更新日期：1989-08-01 00:00:00

abstract：:The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting p...

journal_title：Journal of biomolecular structure & dynamics

authors： Stellwagen NC,Stellwagen D

更新日期：1990-12-01 00:00:00

abstract：:Phospholipase A(2) belongs to a super family of enzymes that is massively over expressed in a variety of severe inflammatory diseases, which degrades membrane phospholipids. It has also been reported that this activity leads to loss of tissue, organ integrity and function. This enzyme is an important target for anti-i...

journal_title：Journal of biomolecular structure & dynamics

authors： Ompraba G,Velmurugan D,Louis PA,Rafi ZA

更新日期：2010-02-01 00:00:00

abstract：:Over the last few years, some novel researches in the field of medical science made a tendency to have a therapy without any complications or side-effects of the disease with the aid of prognosis about the behaviors of the substructure living biological cell. Regarding this issue, nonlinear frequency characteristics o...

journal_title：Journal of biomolecular structure & dynamics

authors： Najaafi N,Jamali M,Habibi M,Sadeghi S,Jung DW,Nabipour N

更新日期：2020-04-17 00:00:00

abstract：:The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from natural plant sources is an area of immense potential. The curre...

journal_title：Journal of biomolecular structure & dynamics

authors： Wahedi HM,Ahmad S,Abbasi SW

更新日期：2020-05-12 00:00:00

abstract：:In the present work fluctuations of number of ligands adsorbed on macromolecule are investigated. We have taken into account the adsorption and desorption of ligands under the circumstance of some adsorption centers fluctuations affected by medium fluctuation. The correlation function and spectral density of number of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arakelyan VB,Haroutiunian SG,Arakelyan HV,Haroutiunian TS

更新日期：2002-08-01 00:00:00

abstract：:The conformational space available to GnRH and lGnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calcu...

journal_title：Journal of biomolecular structure & dynamics

authors： Watts CR,Mezei M,Murphy RF,Lovas S

更新日期：2001-04-01 00:00:00

abstract：:The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Barton JK

更新日期：1983-12-01 00:00:00

abstract：:We have examined the conformational energetics of the eight most commonly occurring nucleosides--A, U, G, C, dA, dT, dG, dC--as monitored by a semi-empirical energy force field. These are the first reported calculations to completely explore the entire conformational spaces available to all eight major nucleosides usi...

journal_title：Journal of biomolecular structure & dynamics

authors： Pearlman DA,Kim SH

更新日期：1985-08-01 00:00:00

abstract：:The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were con...

journal_title：Journal of biomolecular structure & dynamics

authors： Ponnuswamy PK,Anukanth A

更新日期：1989-02-01 00:00:00

abstract：:SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodoc...

journal_title：Journal of biomolecular structure & dynamics

authors： Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik I

更新日期：2020-11-17 00:00:00

abstract：:p21-activated kinases (Paks) play an integral component in various cellular diverse processes. The full activation of Pak is dependent upon several serine residues present in the N-terminal region, a threonine present at the activation loop, and finally the phosphorylation of these residues ensure the complete activat...

journal_title：Journal of biomolecular structure & dynamics

authors： Biswal J,Jayaprakash P,Suresh Kumar R,Venkatraman G,Poopandi S,Rangasamy R,Jeyaraman J

更新日期：2020-01-01 00:00:00

abstract：:The fragile X triplet repeats, (GCC)n x (GGC)n are located at the 5' untranslated region of the FMR-1 gene. Inordinate repeat expansion and hyper-methylation of the CpG islands inside the repeat lead to the suppression of the FMR-1 gene and the subsequent onset and progression of the disease. Previously, we have shown...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen X,Mariappan SV,Moyzis RK,Bradbury EM,Gupta G

更新日期：1998-02-01 00:00:00

abstract：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Anish Babu A,Karthick K,Subramanian R,Swarnalatha K

更新日期：2020-08-01 00:00:00

abstract：:It is well established that GAA/TTC base triplet expansion is the cause of degenerative disorder in Freidreich's Ataxia. It is also known that these repeat sequences fold back to form the unusual intramolecular triple helix structures in DNA of the type Pyrimidine *Purine *Pyrimidine or Purine *Purine*Pyrimidine. In t...

journal_title：Journal of biomolecular structure & dynamics

authors： Jain A,Rajeswari MR,Ahmed F

更新日期：2002-02-01 00:00:00