BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC).

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：:Enzymes involved in the pyrimidine biosynthesis pathway have become an important target for the pharmacological intervention. One among those enzymes, Aspartate Trans Carbamoylase (ATCase), catalyses the condensation of aspartate and carbamoyl phosphate to form N-carbamoyl-l-aspartate and inorganic phosphate. The pres...

journal_title：Journal of biomolecular structure & dynamics

authors： Kanagarajan S,Mutharasappan N,Dhamodharan P,Jeyaraman M,Ramadas K,Jeyaraman J

更新日期：2014-04-01 00:00:00

abstract：:The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition patte...

journal_title：Journal of biomolecular structure & dynamics

authors： Florián J,Leszczyński J

更新日期：1995-04-01 00:00:00

abstract：:MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) are modular proteins covalently anchored in the bacterial cell wall of many Gram-positive bacteria. The N-terminal region of most MSCRAMMs carries the ligand-binding domains (A region) which specifically target the host extracellular matrix ...

journal_title：Journal of biomolecular structure & dynamics

authors： Jemima Beulin DS,Ponnuraj K

更新日期：2017-02-01 00:00:00

abstract：:The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density fu...

journal_title：Journal of biomolecular structure & dynamics

authors： Shiri F,Hadidi S,Rahimi-Nasrabadi M,Ahmadi F,Ganjali MR,Ehrlich H

更新日期：2020-03-01 00:00:00

abstract：:NAD(P)H: quinone oxidoreductase 1 (NQO1) inhibitors are proved as promising therapeutic agents against cancer. This study is to determine potent NAD(P)H-dependent NQO1 inhibitors with new scaffold. Pharmacophore-based three-dimensional (3D) QSAR model has been built based on 45 NQO1 inhibitors reported in the literatu...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvakumar R,Anantha Krishnan D,Ramakrishnan C,Velmurugan D,Gunasekaran K

更新日期：2020-02-01 00:00:00

abstract：:A family of covalent complexes between oligonucleotides and derivatives of the intercalating agent 9-amino acridine has been synthesized (Asseline, U., Thuong, N.T. and Helene, C. (1983) C.R.Acad. Sci. (Paris) 297 (III), 369-372) and studied (Lancelot, G., Asseline, U., Thuong, N.T., and Helene, C. (1985) Biochemistry...

journal_title：Journal of biomolecular structure & dynamics

authors： Cieplak P,Rao SN,Hélène C,Montenay-Garestier T,Kollman PA

更新日期：1987-10-01 00:00:00

abstract：:Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...

journal_title：Journal of biomolecular structure & dynamics

authors： Malkhed V,Mustyala KK,Potlapally SR,Vuruputuri U

更新日期：2014-12-01 00:00:00

abstract：:The nucleoprotein (NP) binds the viral RNA genome as oligomers assembled with the polymerase in a ribonucleoprotein complex required for transcription and replication of influenza A virus. Novel antiviral candidates targeting the nucleoprotein either induced higher order oligomers or reduced NP oligomerization by targ...

journal_title：Journal of biomolecular structure & dynamics

authors： Tarus B,Bertrand H,Zedda G,Di Primo C,Quideau S,Slama-Schwok A

更新日期：2015-09-01 00:00:00

abstract：:Tris-intercalation of an acridine trimer into the self-complementary dodecanucleotide d(CTTCGCGCGAAG) has been studied, in solution, by means of 1H and 31P nuclear magnetic resonance. In a first step all the non-exchangeable protons (except H5', H5"), the imino protons and seven of the eleven phosphorus have been assi...

journal_title：Journal of biomolecular structure & dynamics

authors： Laugaa P,Delepierre M,Dupraz B,Igolen J,Roques BP

更新日期：1988-12-01 00:00:00

abstract：:A conceptually new idea in quantitative structure-activity relationships (QSAR) which makes use of ensembles from molecular dynamics (MD) trajectories and information retrieved from enzyme-inhibitor binding thermodynamics is presented in this study. This new methodology, termed ensemble comparative residue interaction...

journal_title：Journal of biomolecular structure & dynamics

authors： Khedkar VM,Joseph J,Pissurlenkar R,Saran A,Coutinho EC

更新日期：2015-01-01 00:00:00

abstract：:EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive 5-iodo-2'-deoxyuridine (i(5)dU) or 5-[4-(3-(trifl...

journal_title：Journal of biomolecular structure & dynamics

authors： Koudan EV,Subach OM,Korshunova GA,Romanova EA,Eritja R,Gromova ES

更新日期：2002-12-01 00:00:00

abstract：:Temporal order ("chronology") of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis of 60 different criteria each offering certain temporal order. After several steps of filtering the chronology vectors are averaged ...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2004-08-01 00:00:00

abstract：:Tropomyosin receptor kinase A (Trk A) is a receptor tyrosine kinase activated by nerve growth factor (NGF). TrkA plays an important role in pain sensation, which leads to significant interest in the development of small molecule inhibitors of TrkA. However, TrkA and the other two highly homologous isoforms, TrkB and T...

journal_title：Journal of biomolecular structure & dynamics

authors： Wu X,Li Q,Wan S,Zhang J

更新日期：2021-01-01 00:00:00

abstract：:The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-t...

journal_title：Journal of biomolecular structure & dynamics

authors： Chandrasekaran R,Giacometti A,Arnott S

更新日期：2000-06-01 00:00:00

abstract：:We have applied random-search, energy minimization and molecular dynamics simulations to investigate the structural aspects of the interaction of N-acetyl-L-prolyl-D-alanyl-L-alanine-N'-methylamide with Ca2+. Spectral data on related peptides had suggested that the beta-turn conformation might be a prerequisite for th...

journal_title：Journal of biomolecular structure & dynamics

authors： Michel AG,Jeandenans C,Ananthanarayanan VS

更新日期：1992-10-01 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：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Ganjoo A,Tripathi A,Chetti P

更新日期：2020-10-01 00:00:00

abstract：:Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(...

journal_title：Journal of biomolecular structure & dynamics

authors： Poltev VI,Teplukhin AV,Chuprina VP

更新日期：1988-12-01 00:00:00

abstract：:Ebola virus (EboV) is currently ravaging West Africa with estimated case fatality rate of 52%. Currently, no drug treatment is available and immunoglobulin therapy is still at the rudimentary stage. For anti-EboV drug development, druggable viral and host protein targets, including human Furin are under intense invest...

journal_title：Journal of biomolecular structure & dynamics

authors： Omotuyi IO

更新日期：2015-01-01 00:00:00

abstract：:Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

journal_title：Journal of biomolecular structure & dynamics

authors： Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

更新日期：2020-11-02 00:00:00

abstract：:Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Berger I,Spačková N,Leszczynski J,Hobza P

更新日期：2000-01-01 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：:Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from trad...

journal_title：Journal of biomolecular structure & dynamics

authors： Sun MF,Chang TT,Chang KW,Huang HJ,Chen HY,Tsai FJ,Lin JG,Chen CY

更新日期：2011-06-01 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：:Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) sim...

journal_title：Journal of biomolecular structure & dynamics

authors： Song W,Guo JT

更新日期：2015-01-01 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：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

更新日期：2020-11-06 00:00:00

abstract：:Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that t...

journal_title：Journal of biomolecular structure & dynamics

authors： Premraj BJ,Yathindra N

更新日期：1998-10-01 00:00:00

abstract：:In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic cont...

journal_title：Journal of biomolecular structure & dynamics

authors： Agudelo D,Bourassa P,Bariyanga J,Tajmir-Riahi HA

更新日期：2018-12-01 00:00:00