Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

abstract：:K562 cells are erythroleukemic cells derived from a chronic myeloid leukemia patient in blast crisis. Comparison of the genome from K562 cells and normal human genome has been very useful strategy, in uncovering eight genes, implicated in acute myeloid leukemia (AML). These genes carry mutations in K562 genome and the...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh D,Saha C,Hossain M,Dey SK,Kumar GS

更新日期：2013-03-01 00:00:00

abstract：:Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

journal_title：Journal of biomolecular structure & dynamics

authors： Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

更新日期：1994-08-01 00:00:00

abstract：:The coexistence of both A form and B form tracts and formation of an A-B junction in the oligomer d(GGGGGTTTTT).d(AAAAACCCCC) in saturated sodium chloride solution have been detected by Raman spectroscopy. The entire duplex adopts the familiar B-form conformation in aqueous solution at low salt concentrations (0.1M Na...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang Y,Thomas GA,Peticolas WL

更新日期：1989-06-01 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：:DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide ...

journal_title：Journal of biomolecular structure & dynamics

authors： Brukner I,Sánchez R,Suck D,Pongor S

更新日期：1995-10-01 00:00:00

abstract：:Noonan syndrome (NS) is a common autosomal dominant congenital disorder which could cause the congenital cardiopathy and cancer predisposition. Previous studies reported that the knock-in mouse models of the mutant D61G of SHP2 exhibited the major features of NS, which demonstrated that the mutation D61G of SHP2 could...

journal_title：Journal of biomolecular structure & dynamics

authors： Li HL,Ma Y,Zheng CJ,Jin WY,Liu WS,Wang RL

更新日期：2018-11-01 00:00:00

abstract：:The hypothetical protection of genes from oxidative damage provided by the G-rich telomeric overhangs located at the end of chromosomes, which consist, in humans, of single strands of TTAGGG sequence repeats, is investigated here. First principle Moller-Plesset perturbation theory calculations reveal that the TTAGGG h...

journal_title：Journal of biomolecular structure & dynamics

authors： Cauët E

更新日期：2011-12-01 00:00:00

abstract：:The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant...

journal_title：Journal of biomolecular structure & dynamics

authors： Sérgio Alves Bueno P,Carina Biavatti D,Sandro Gularte Chiarello A,Aureliana Fassina V,Aparecida Fernandez M,Augusto Vicente Seixas F

更新日期：2019-09-01 00:00:00

abstract：:The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...

journal_title：Journal of biomolecular structure & dynamics

authors： Almeida JSFD,Botelho FD,de Souza FR,Dos Santos MC,Goncalves ADS,Rodrigues RLB,Cardozo M,Kitagawa DAS,Vieira LA,Silva RSF,Cavalcante SFA,Bastos LDC,Nogueira MOT,de Santana PIR,Brum JOC,Nepovimova E,Kuca K,LaPlante SR,G

更新日期：2021-01-08 00:00:00

abstract：:The so-called CCAAT box is believed to be a major promoter element of higher eukaryotes though it is ill-defined being deduced from very limited sequence data. The comprehensive computer analysis of an unbiased set of 168 promoters presented here removes several of the persisting uncertainties. In particular, it delin...

journal_title：Journal of biomolecular structure & dynamics

authors： Bucher P,Trifonov EN

更新日期：1988-06-01 00:00:00

abstract：:A mononuclear cadmium(II) complex of formula [Cd(5,5'-dmbipy)2(OAc)2]·2H2O (5,5'-dmbipy = 5,5'-dimethyl-2,2'-bipyridine and OAc = acetato ligand) has been synthesized and characterized by FT-IR, UV-Vis, 1H-NMR, elemental analysis and single-crystal X-ray structure analysis. The molecular structure of the complex shows...

journal_title：Journal of biomolecular structure & dynamics

authors： Kondori T,Akbarzadeh-T N,Abdi K,Dušek M,Eigner V

更新日期：2020-01-01 00:00:00

abstract：:It is generally believed that base-pair stacking interaction in DNA double helix is one of the strongest interactions that governs sequence directed structural variability. However, X-ray crystal structures of some base-paired doublet sequences have been seen to adopt different structures when flanked by different bas...

journal_title：Journal of biomolecular structure & dynamics

authors： Bandyopadhyay D,Bhattacharyya D

更新日期：2000-08-01 00:00:00

abstract：:NPC1 is a 25-exon gene located on the long arm of chromosome 18q11.2 and encodes NPC1, a transmembrane protein comprising 1278 amino acid residues. Mutations in the NPC1 gene can cause Niemann-Pick disease type C (NP-C), a rare autosomal-recessive neurovisceral disease. We assessed mutant protein folding using compute...

journal_title：Journal of biomolecular structure & dynamics

authors： Martínez-Archundia M,Hernández Mojica TG,Correa-Basurto J,Montaño S,Camacho-Molina A

更新日期：2020-08-01 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：:Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of fre...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen C,Huang Y,Xiao Y

更新日期：2013-01-01 00:00:00

abstract：:Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...

journal_title：Journal of biomolecular structure & dynamics

authors： Murphy D,Doyle H,Eritja R,Redmond G

更新日期：2004-10-01 00:00:00

abstract：:Chlamydia trachomatis (C.t) is a major causative of infectious blindness in world. It is a real challenge to combat Chlamydial infection as it is an intracellular pathogen. Hence, it is essential to determine the most potential targets of C.t in order to inhibit or suppress its virulence during its infectious phase. T...

journal_title：Journal of biomolecular structure & dynamics

authors： Sadhasivam A,Nagarajan H,Umashankar V

更新日期：2020-07-01 00:00:00

abstract：:Triple-negative breast cancers (TNBCs) are one of the most aggressive and complex forms of cancers in women. TNBCs are commonly known for their complex heterogeneity and poor prognosis. The present work aimed to develop a predictive 2D and 3D quantitative structure-activity relationship (QSAR) models against metastati...

journal_title：Journal of biomolecular structure & dynamics

authors： Shukla A,Tyagi R,Meena S,Datta D,Srivastava SK,Khan F

更新日期：2020-01-01 00:00:00

abstract：:A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibi...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehraban MH,Odooli S,Yousefi R,Roghanian R,Motovali-Bashi M,Moosavi-Movahedi AA,Ghasemi Y

更新日期：2017-07-01 00:00:00

abstract：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Huertas D,Lipps H,Azorín F

更新日期：1994-08-01 00:00:00

abstract：:Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker, and Hex-Cuda, to study the effect of alteration in the structure of carbamate-based acetylcholyne esterase (AChE) inhibitors. Sixteen selected systems were then subjected to 14 ns m...

journal_title：Journal of biomolecular structure & dynamics

authors： Mohammadi T,Ghayeb Y

更新日期：2018-01-01 00:00:00

abstract：:Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-gly...

journal_title：Journal of biomolecular structure & dynamics

authors： Mamidi AS,Surolia A

更新日期：2015-01-01 00:00:00

abstract：:The Transformer2 (Tra2) proteins in humans are homologues of the Drosophila Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh P,Grellscheid SN,Sowdhamini R

更新日期：2016-09-01 00:00:00

abstract：:Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...

journal_title：Journal of biomolecular structure & dynamics

authors： Borkar A,Rout MK,Hosur RV

更新日期：2012-01-01 00:00:00

abstract：:Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear r...

journal_title：Journal of biomolecular structure & dynamics

authors： Pyshnyi DV,Goldberg EL,Ivanova EM

更新日期：2003-12-01 00:00:00

abstract：:The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentati...

journal_title：Journal of biomolecular structure & dynamics

authors： Frenkel ZM,Trifonov EN

更新日期：2005-06-01 00:00:00

abstract：:Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on a...

journal_title：Journal of biomolecular structure & dynamics

authors： Chakrabarti B,Bairagya HR,Mallik P,Mukhopadhyay BP,Bera A

更新日期：2011-02-01 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：:Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolaskar AS,Joshi RR

更新日期：1998-06-01 00:00:00

abstract：:A number of tandemly repeated DNA sequences have the ability to form hairpin structures by forming non-standard base pairs. When (GCC)15 and (GGC)15 strands are annealed together, the expected duplex is the only product. However, when (GCC)15 is annealed with (GCC)10, depending on the relative concentrations, up to fi...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao Y,Cheng W,Gibb CL,Gupta G,Kallenbach NR

更新日期：1996-10-01 00:00:00