Using recurrence quantification analysis descriptors for protein sequence classification with support vector machines.

abstract：:Human β-defensin-3 (HβD-3) is an endogenous antimicrobial peptide with potent and broad killing activity against various microorganisms, and thus, it is an attractive candidate for the development of novel peptide antibiotics, but its antimicrobial mechanism remains elusive. To characterize the mechanism, we used mult...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao X,Yu H,Yang L,Li Q,Huang X

更新日期：2015-01-01 00:00:00

abstract：:To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guano...

journal_title：Journal of biomolecular structure & dynamics

authors： Markova N,Pejov L,Stoyanova N,Enchev V

更新日期：2017-05-01 00:00:00

abstract：:Non-obstructive azoospermia (NOA) is the most clinical problem in case of infertility. About 70% of NOA patients are idiopathic with uncharacterized molecular mechanisms. This study aimed to analyze the possible pathogenic miRNA-target gene interaction and lncRNA-miRNA association involved in NOA. In the current study...

journal_title：Journal of biomolecular structure & dynamics

authors： Sabetian S,Zarei M,Jahromi BN,Morowvat MH,Tabei SMB,Cava C

更新日期：2021-01-26 00:00:00

abstract：:Mycobacterium tuberculosis remains one of the most successful bacterial pathogens worldwide. The development of drug-resistant strains and the ability of the bacteria to persist in a latent form in the host are major problems for tuberculosis (TB) control. Glyoxylate shunt is a metabolic bypass of the Krebs cycle and ...

journal_title：Journal of biomolecular structure & dynamics

authors： Shukla R,Shukla H,Tripathi T

更新日期：2020-04-30 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：: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：:The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1...

journal_title：Journal of biomolecular structure & dynamics

authors： Golovanov EuI,Kalambet YuA,Auezova LJ,Alexandrov AA

更新日期：1986-06-01 00:00:00

abstract：:Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhattacharjee A,Hossain MU,Chowdhury ZM,Rahman SMA,Bhuyan ZA,Salimullah M,Keya CA

更新日期：2020-03-11 00:00:00

abstract：:Drug resistant mutations have severely restricted the success of HIV therapy. These mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lastin...

journal_title：Journal of biomolecular structure & dynamics

authors： Purohit R,Rajendran V,Sethumadhavan R

更新日期：2011-08-01 00:00:00

abstract：:Time Correlated Single Photon Counting (TCSPC) was used for the first time to analyze the effect/changes in the mode of intercalation of ethidium bromide (EtBr) and acridine orange (AO) to calf thymus DNA brought about due to interaction of naturally occurring methylxanthines such as theophylline (X1), theobromine (X2...

journal_title：Journal of biomolecular structure & dynamics

authors： Johnson IM,Kumar SG,Malathi R

更新日期：2003-04-01 00:00:00

abstract：:Two 4-ns molecular dynamics simulations of calcium loaded calmodulin in solution have been performed, using both standard nonbonded cutoffs and Ewald summation to treat electrostatic interactions. Our simulation results are generally consistent with solution experimental studies of calmodulin structure and dynamics, i...

journal_title：Journal of biomolecular structure & dynamics

authors： Yang C,Jas GS,Kuczera K

更新日期：2001-10-01 00:00:00

abstract：:Cromolyn sodium (CS), an anti-inflammatory drug is used in the treatment of allergic disorders. Bovine serum albumin (BSA) a blood plasma protein is used as a model protein for studying protein folding and ligand binding mechanism as it is the main transporter protein which decides the disposition and pharmacodynamics...

journal_title：Journal of biomolecular structure & dynamics

authors： Yasmeen S,Riyazuddeen,Khatun S,Abul Qais F

更新日期：2020-02-01 00:00:00

abstract：:A simple statistical approach for the analysis of biological sequences, such as splice-sites, promoter regions, helices and extended structure forming regions or any other sequence dependent functional entities in proteins, is presented. The approach has been proved useful to develop a method for prediction of such en...

journal_title：Journal of biomolecular structure & dynamics

authors： Reddy BV,Pandit MW

更新日期：1995-02-01 00:00:00

abstract：:Trypanothione reductase has long been investigated as a promising target for chemotherapeutic intervention in Chagas disease, since it is an enzyme of a unique metabolic pathway that is exclusively present in the pathogen but not in the human host, which has the analog Glutathione reductase. In spite of the present da...

journal_title：Journal of biomolecular structure & dynamics

authors： de Paula da Silva CH,Bernardes LS,da Silva VB,Zani CL,Carvalho I

更新日期：2012-01-01 00:00:00

abstract：:Phytoestrogens are dietary estrogens having similar structure as of estrogen. Some of these phytoestrogens are androgen receptor (AR) antagonists and exhibit preventive role in the prostate cancer. However, in androgen-independent prostate cancer (AIPC) the ARs were mutated (T877A, W741L, F876L, etc.) and these mutant...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvaraj D,Muthu S,Kotha S,Siddamsetty RS,Andavar S,Jayaraman S

更新日期：2021-02-01 00:00:00

abstract：:MutSα is the most abundant mismatch-binding factor of human DNA mismatch repair (MMR) proteins. MMR maintains genetic stability by recognizing and repairing DNA defects. Failure to accomplish their function may lead to cancer. In addition, MutSα recognizes at least some types of DNA damage making it a target for antic...

journal_title：Journal of biomolecular structure & dynamics

authors： Negureanu L,Salsbury FR Jr

更新日期：2014-01-01 00:00:00

abstract：:Acinetobacter baumannii, an important nosocomial pathogen, is increasingly becoming resistant to antibiotics including recent β-lactam like imipenem. Production of different types of β-lactamases is one of the major resistance mechanisms which bacteria adapt. We recently reported the presence of a β-lactamase, OXA-51,...

journal_title：Journal of biomolecular structure & dynamics

authors： Tiwari V,Moganty RR

更新日期：2014-01-01 00:00:00

abstract：:A theoretical study is presented of the energetic and structural properties of covalent adducts of benzo[a]pyrene and a DNA fragment. Energy optimisation is performed with the use of minimiser with constraints and an advanced semiempirical energy formula. Three types of adducts are studied: an external complex with th...

journal_title：Journal of biomolecular structure & dynamics

authors： Zakrzewska K,Pullman B

更新日期：1987-04-01 00:00:00

abstract：:We have analysed S1 sensitivity of SV40 minichromosomes isolated from the nuclei of infected cells at the late stage of infection. We show that a fraction of purified minichromosomes is sensitive towards double-strand cleavage by S1 nuclease. The pattern of specific cleavage reminiscent of that found for subcloned fra...

journal_title：Journal of biomolecular structure & dynamics

authors： Nedospasov SA,Shakhov AN,Hirt B

更新日期：1989-04-01 00:00:00

abstract：:Epidermal growth factor (EGF) plays important roles in multiple biological processes, such as the regulation of cell growth, proliferation, and differentiation. EGF exerts their pharmacologic effects via receptor-mediated mechanism associated with high affinity to epidermal growth factor receptor (EGFR) on the cell su...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehrabi M,Khodarahmi R,Shahlaei M

更新日期：2017-04-01 00:00:00

abstract：:X-chromosome-linked inhibitor of apoptosis (XIAP) inhibits cell apoptosis. Overexpression of XIAP is widely found in human cancers. Second mitochondria-derived activator of caspase (SMAC) protein inhibits XIAP through binding with Baculovirus Inhibitor of apoptosis protein Repeat (BIR) 3 or BIR2 domain of XIAP. In thi...

journal_title：Journal of biomolecular structure & dynamics

authors： Tian S,Ji C,Zhang JZH

更新日期：2021-02-01 00:00:00

abstract：:The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conserv...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh SK,Saha B,Banerjee R

更新日期：2020-07-08 00:00:00

abstract：:Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by in silico experiments. Switches from t...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolomiets IN,Zarudnaya MI,Potyahaylo AL,Hovorun DM

更新日期：2015-01-01 00:00:00

abstract：:We have performed an 4-ns MD simulation of calmodulin complexed with a target peptide in explicit water, under realistic conditions of constant temperature and pressure, in the presence of a physiological concentration of counterions and using Ewald summation to avoid truncation of long-range electrostatic forces. Dur...

journal_title：Journal of biomolecular structure & dynamics

authors： Yang C,Kuczera K

更新日期：2002-10-01 00:00:00

abstract：:Partial proteolysis of the lambda cI repressor has been carried out systematically with trypsin, chymotrypsin, elastase, endoproteinase Glu-C, kallikrein, and thrombin. The cleavage sites have been determined by (i) comparison of fragments produced and observed in SDS-polyacrylamide gel with known fragments and plots ...

journal_title：Journal of biomolecular structure & dynamics

authors： Pal A,Chattopadhyaya R

更新日期：2008-12-01 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：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kargatov AM,Efimov AV

更新日期：2020-03-01 00:00:00

abstract：:The present paper describes design, synthesis, and biological evaluation of a series of some 3-[3-(amino)propoxy]benzenamines as acetylcholinesterase inhibitors using mice as a model and piracetam as a reference drug. The structures of these compounds were confirmed by spectral analysis and compounds were tested for m...

journal_title：Journal of biomolecular structure & dynamics

authors： Malik R,Gupta R,Srivastava S,Choudhary BS,Sharma M

更新日期：2017-08-01 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：: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