Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex
نویسندگان
چکیده
منابع مشابه
Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex
The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nuclei...
متن کاملMolecular Docking and Molecular Dynamics Study of DNA Minor Groove Binders
The fundamental problems in drug discovery are based on the process of molecular recognition by small molecules. The binding specificity of DNA-small molecule is identified mainly by studying the hydrogen bonding and polar interactions. Majority of the minor groove binders and their mechanism of action at the molecular level are not well studied. As these small molecules can act as effective th...
متن کاملSurflex-related material 1. Ajay N. Jain. Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search
The Surflex flexible molecular docking method has been generalized and extended in two primary areas related to the search component of docking. First, incorporation of a small-molecule force-field extends the search into Cartesian coordinates constrained by internal ligand energetics. Whereas previous versions searched only the alignment and acyclic torsional space of the ligand, the new appro...
متن کاملMolecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analogues.
By hindering or "silencing" protein translation in vivo, antisense nucleic acid analogues that hybridize to bacterial rRNA could serve as a promising class of antibacterial compounds. Thus, we performed a comparative analysis of the dynamical properties of modified oligonucleotides based upon a sequence (5')r(UGUUACGACU)(3') that is complementary to bacterial ribosomal A-site RNA. In particular...
متن کاملsynthesis of amido alkylnaphthols using nano-magnetic particles and surfactants
we used dbsa and nano-magnetic for the synthesis of amido alkylnaphtols.
15 صفحه اولذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Information and Modeling
سال: 2008
ISSN: 1549-9596,1549-960X
DOI: 10.1021/ci800063v