Search Results - "Banavali, N"

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution by Banavali, Nilesh K, Roux, Benoît

“…The interconversion between the well-characterized A- and B-forms of DNA is a structural transition for which the intermediate states and the free energy…”
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Free Energy and Structural Pathways of Base Flipping in a DNA GCGC Containing Sequence by Banavali, Nilesh K, MacKerell, Alexander D

“…Structural distortions of DNA are essential for its biological function due to the genetic information of DNA not being physically accessible in the duplex…”
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Protein-Facilitated Base Flipping in DNA by Cytosine-5-Methyltransferase by Huang, Niu, Banavali, Nilesh K., MacKerell, Alexander D.

“…DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of DNA as required for transcription and replication are initiated by…”
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Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids by Banavali, Nilesh K, MacKerell, Alexander D

“…The anomeric effect in the phosphodiester backbone of nucleic acids is a stereoelectronic effect that has conventionally been linked to interactions between…”
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Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA by Banavali, N K, MacKerell, A D

“…Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been…”
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Development and Current Status of the CHARMM Force Field for Nucleic Acids by MacKerell, AD Jr, Banavali, N, Foloppe, N

“…The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field…”
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Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets To Probe the Mechanism of Base Flipping by HhaI DNA (Cytosine C5)-methyltransferase by Wang, Peiyuan, Brank, Adam S, Banavali, Nilesh K, Nicklaus, Marc C, Marquez, Victor E, Christman, Judith K, MacKerell, Alexander D

“…X-ray crystallographic studies of HhaI DNA (cytosine-C5)-methyltransferase (M.HhaI) covalently linked to methylated 5-fluorocytosine in DNA provided the first…”
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Development and current status of the CHARMM force field for nucleic acids by MacKerell Jr, Alexander D., Banavali, Nilesh, Foloppe, Nicolas

“…The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field…”
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Cloning and characterization of the gene encoding 1-cyclohexenylcarbonyl coenzyme A reductase from Streptomyces collinus by Wang, P, Denoya, C D, Morgenstern, M R, Skinner, D D, Wallace, K K, Digate, R, Patton, S, Banavali, N, Schuler, G, Speedie, M K, Reynolds, K A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution by MacKerell, Alexander D., Banavali, Nilesh K.

“…Molecular dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in solution. Presented are…”
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INHIBITION OF (CYTOSINE C5)-METHYLTRANSFERASE BY OLIGONUCLEOTIDES CONTAINING FLEXIBLE (CYCLOPENTANE) AND CONFORMATIONALLY CONSTRAINED (BICYCLO[3.1.0]HEXANE) ABASIC SITES by Marquez, Victor E., Wang, Peiyuan, Nicklaus, Marc C., Maier, Martin, Manoharan, Muthiah, Christman, Judith K., Banavali, Nilesh K., Mackerell, Alexander D.

“…Pseudorotationally locked sugar analogues based on bicyclo[3.1.0]-hexane templates were placed in DNA duplexes as abasic target sites in the M.HhaI recognition…”
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The N-Terminal End of the Catalytic Domain of Src Kinase Hck Is a Conformational Switch Implicated in Long-Range Allosteric Regulation by Banavali, Nilesh K., Roux, Benoît

“…Signal transduction in cell growth and proliferation involves regulation of kinases through long-range allostery between remote protein regions. Molecular…”
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Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase by Horton, John R., Ratner, Gary, Banavali, Nilesh K., Huang, Niu, Choi, Yongseok, Maier, Martin A., Marquez, Victor E., MacKerell, Alexander D., Cheng, Xiaodong

“…Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket (‘base flipping’) is a mechanistic feature common to some DNA/RNA-binding…”
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Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids by Banavali, Nilesh K, Roux, Benoıt

“…The accuracy of continuum electrostatic models, in which the solvent is represent as a featureless dielectric medium, depends sensitively on the choice of the…”
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