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Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations
R Rohs, I Bloch, H Sklenar, Z Shakked - Nucleic acids research, 2005 - academic.oup.com
The dynamics of biological processes depend on the structure and flexibility of the
interacting molecules. In particular, the conformational diversity of DNA allows for large …
interacting molecules. In particular, the conformational diversity of DNA allows for large …
HIV‐1 integrase inhibitors: 2003–2004 update
R Dayam, J Deng, N Neamati - Medicinal research reviews, 2006 - Wiley Online Library
The integration of viral cDNA into the host genome is an essential step in the HIV‐1‐life
cycle and is mediated by the virally encoded enzyme, integrase (IN). Inhibition of this …
cycle and is mediated by the virally encoded enzyme, integrase (IN). Inhibition of this …
Complex of linker histone H5 with the nucleosome and its implications for chromatin packing
L Fan, VA Roberts - Proceedings of the National Academy of Sciences, 2006 - pnas.org
Linker histones are essential for chromatin filament formation, and they play key roles in the
regulation of gene expression. Despite the determination of structures of the nucleosome …
regulation of gene expression. Despite the determination of structures of the nucleosome …
DOT2: Macromolecular docking with improved biophysical models
VA Roberts, EE Thompson, ME Pique… - Journal of …, 2013 - Wiley Online Library
Computational docking is a useful tool for predicting macromolecular complexes, which are
often difficult to determine experimentally. Here, we present the DOT2 software suite, an …
often difficult to determine experimentally. Here, we present the DOT2 software suite, an …
Could quantum mechanical properties be reflected on classical molecular dynamics? the case of halogenated organic compounds of biological interest
Essential to understanding life, the biomolecular phenomena have been an important
subject in science, therefore a necessary path to be covered to make progress in human …
subject in science, therefore a necessary path to be covered to make progress in human …
Mononuclear silver (I) complexes with 1, 7-phenanthroline as potent inhibitors of Candida growth
Mononuclear silver (I) complexes with 1, 7-phenanthroline (1, 7-phen),[Ag (NO 3-O, O′)(1,
7-phen-N7) 2](1) and [Ag (1, 7-phen-N7) 2] X, X= ClO 4−(2), CF 3 SO 3−(3), BF 4−(4) and …
7-phen-N7) 2](1) and [Ag (1, 7-phen-N7) 2] X, X= ClO 4−(2), CF 3 SO 3−(3), BF 4−(4) and …
In-Silicodocking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate
A Savarino - Retrovirology, 2007 - Springer
Abstract Background HIV-1 integrase (IN) is an emerging drug target, as IN strand transfer
inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials. One credible …
inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials. One credible …
Genetic analyses of DNA-binding mutants in the catalytic core domain of human immunodeficiency virus type 1 integrase
R Lu, A Limón, HZ Ghory, A Engelman - Journal of virology, 2005 - journals.asm.org
The catalytic core domain (CCD) of human immunodeficiency virus type 1 (HIV-1) integrase
(IN) harbors the enzyme active site and binds viral and chromosomal DNA during …
(IN) harbors the enzyme active site and binds viral and chromosomal DNA during …
Synthesis, cytotoxic activity and DNA interaction studies of new dinuclear platinum (ii) complexes with an aromatic 1, 5-naphthyridine bridging ligand: DNA binding …
B Konovalov, MD Živković, JZ Milovanović… - Dalton …, 2018 - pubs.rsc.org
The synthesis, spectroscopic characterization, cytotoxic activity and DNA binding evaluation
of seven new dinuclear platinum (II) complexes Pt1–Pt7, with the general formula [{Pt (L) Cl} …
of seven new dinuclear platinum (II) complexes Pt1–Pt7, with the general formula [{Pt (L) Cl} …
Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK's performance
The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long
been challenges that prevented the development of efficient protein–DNA docking methods …
been challenges that prevented the development of efficient protein–DNA docking methods …