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Nilesh K. Banavali - Publications

Affiliations: 
Biomedical Sciences State University of New York, Albany, Albany, NY, United States 
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Banavali NK. The Mechanism of Cholesterol Modification of Hedgehog Ligand. Journal of Computational Chemistry. 41: 520-527. PMID 31823413 DOI: 10.1002/Jcc.26097  0.337
2019 Zhao J, Ciulla DA, Xie J, Castillo DA, Wagner A, Zwarycz AS, Lin Z, Beadle S, Giner JL, Li Z, Li H, Banavali N, Callahan BP, Wang C. General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing. Journal of the American Chemical Society. PMID 31682419 DOI: 10.1021/Jacs.9B08914  0.352
2019 Green CM, Li Z, Smith AD, Novikova O, Bacot-Davis VR, Gao F, Hu S, Banavali NK, Thiele DJ, Li H, Belfort M. Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing. Plos Biology. 17: e3000104. PMID 31600193 DOI: 10.1371/Journal.Pbio.3000104  0.343
2019 Ciulla DA, Wagner AG, Liu X, Cooper CL, Jorgensen MT, Wang C, Goyal P, Banavali NK, Pezzullo JL, Giner JL, Callahan BP. Sterol A-ring plasticity in hedgehog protein cholesterolysis supports a primitive substrate selectivity mechanism. Chemical Communications (Cambridge, England). PMID 30672911 DOI: 10.1039/C8Cc09729A  0.329
2018 Lennon CW, Stanger M, Banavali NK, Belfort M. Conditional Protein Splicing Switch in Hyperthermophiles through an Intein-Extein Partnership. Mbio. 9. PMID 29382734 DOI: 10.1128/Mbio.02304-17  0.363
2018 Manjari SR, Banavali NK. Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. Journal of Chemical Information and Modeling. 58: 453-463. PMID 29357231 DOI: 10.1021/Acs.Jcim.7B00699  0.316
2017 Sedova A, Banavali NK. Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands. Biochemistry. 56: 1426-1443. PMID 28187685 DOI: 10.1021/Acs.Biochem.6B01101  0.744
2016 Bassen DM, Hou Y, Bowser SS, Banavali NK. Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera. Scientific Reports. 6: 31723. PMID 27539392 DOI: 10.1038/Srep31723  0.338
2016 Sedova A, Banavali NK. RNA approaches the B-form in stacked single strand dinucleotide contexts. Biopolymers. 105: 65-82. PMID 26443416 DOI: 10.1002/Bip.22750  0.728
2015 Brecher M, Chen H, Li Z, Banavali NK, Jones SA, Zhang J, Kramer LD, Li H. Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase. Acs Infectious Diseases. 1: 340-349. PMID 26726314 DOI: 10.1021/Acsinfecdis.5B00070  0.314
2015 Brecher M, Chen H, Liu B, Banavali NK, Jones SA, Zhang J, Li Z, Kramer LD, Li H. Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase. Plos One. 10: e0130062. PMID 26098995 DOI: 10.1371/Journal.Pone.0130062  0.314
2014 Manjari SR, Pata JD, Banavali NK. Cytosine unstacking and strand slippage at an insertion-deletion mutation sequence in an overhang-containing DNA duplex. Biochemistry. 53: 3807-16. PMID 24854722 DOI: 10.1021/Bi500189G  0.496
2013 Banavali NK. Analyzing the relationship between single base flipping and strand slippage near DNA duplex termini. The Journal of Physical Chemistry. B. 117: 14320-8. PMID 24206351 DOI: 10.1021/Jp408957C  0.504
2013 Chen H, Zhou B, Brecher M, Banavali N, Jones SA, Li Z, Zhang J, Nag D, Kramer LD, Ghosh AK, Li H. S-adenosyl-homocysteine is a weakly bound inhibitor for a flaviviral methyltransferase. Plos One. 8: e76900. PMID 24130807 DOI: 10.1371/Journal.Pone.0076900  0.323
2013 Banavali NK. Partial base flipping is sufficient for strand slippage near DNA duplex termini. Journal of the American Chemical Society. 135: 8274-82. PMID 23692220 DOI: 10.1021/Ja401573J  0.558
2013 Chen H, Liu L, Jones SA, Banavali N, Kass J, Li Z, Zhang J, Kramer LD, Ghosh AK, Li H. Selective inhibition of the West Nile virus methyltransferase by nucleoside analogs. Antiviral Research. 97: 232-9. PMID 23267828 DOI: 10.1016/J.Antiviral.2012.12.012  0.316
2013 Manjari SR, Banavali NK. 189 Structural articulation of biochemical reactions using altered bonds and iterative topology switching Journal of Biomolecular Structure & Dynamics. 31: 121-122. DOI: 10.1080/07391102.2013.786431  0.37
2013 Zhu L, Zhong X, Chen SRW, Banavali N, Liu Z. Modeling a Ryanodine Receptor Amino-Terminal Domain Connecting the Central Vestibule and the Corner Clamp Region Biophysical Journal. 104: 4-4. DOI: 10.1016/J.Bpj.2012.11.2462  0.312
2012 Zhu L, Zhong X, Chen SR, Banavali N, Liu Z. Modeling a ryanodine receptor N-terminal domain connecting the central vestibule and the corner clamp region. The Journal of Biological Chemistry. 288: 903-14. PMID 23204524 DOI: 10.1074/Jbc.M112.429670  0.321
2011 Yassin AS, Agrawal RK, Banavali NK. Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein. Plos One. 6: e21871. PMID 21779343 DOI: 10.1371/Journal.Pone.0021871  0.361
2011 Yassin AS, Haque ME, Datta PP, Elmore K, Banavali NK, Spremulli LL, Agrawal RK. Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. Proceedings of the National Academy of Sciences of the United States of America. 108: 3918-23. PMID 21368145 DOI: 10.1073/Pnas.1017425108  0.311
2011 Banavali NK. Partial Single Base Flipping is Sufficient to Enable Strand Slippage at DNA Duplex Termini Biophysical Journal. 100: 3-7. DOI: 10.1016/J.Bpj.2010.12.2141  0.521
2010 McNaughton L, Tikhonenko I, Banavali NK, LeMaster DM, Koonce MP. A low affinity ground state conformation for the Dynein microtubule binding domain. The Journal of Biological Chemistry. 285: 15994-6002. PMID 20351100 DOI: 10.1074/Jbc.M109.083535  0.352
2009 Banavali NK, MacKerell AD. Characterizing structural transitions using localized free energy landscape analysis Plos One. 4. PMID 19436759 DOI: 10.1371/Journal.Pone.0005525  0.627
2009 Yang S, Banavali NK, Roux B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proceedings of the National Academy of Sciences of the United States of America. 106: 3776-81. PMID 19225111 DOI: 10.1073/Pnas.0808261106  0.385
2009 Banavali NK, Roux B. Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins. 74: 378-89. PMID 18623061 DOI: 10.1002/Prot.22153  0.318
2008 Banavali NK, Roux B. The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure (London, England : 1993). 13: 1715-23. PMID 16271895 DOI: 10.1016/J.Str.2005.09.005  0.322
2007 Banavali NK, Roux B. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins. 67: 1096-112. PMID 17380483 DOI: 10.1002/Prot.21334  0.337
2007 Macias AT, Banavali NK, MacKerell AD. DNA bending induced by carbocyclic sugar analogs constrained to the north conformation. Biopolymers. 85: 438-49. PMID 17211887 DOI: 10.1002/Bip.20673  0.646
2006 Banavali NK, Huang N, MacKerell AD. Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. The Journal of Physical Chemistry. B. 110: 10997-1004. PMID 16771353 DOI: 10.1021/Jp0561322  0.728
2005 Banavali NK, Roux B. Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. Journal of the American Chemical Society. 127: 6866-76. PMID 15869310 DOI: 10.1021/Ja050482K  0.52
2004 Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Research. 32: 3877-86. PMID 15273274 DOI: 10.1093/Nar/Gkh701  0.747
2003 Huang N, Banavali NK, MacKerell AD. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proceedings of the National Academy of Sciences of the United States of America. 100: 68-73. PMID 12506195 DOI: 10.1073/Pnas.0135427100  0.729
2002 Banavali NK, MacKerell AD. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. Journal of Molecular Biology. 319: 141-60. PMID 12051942 DOI: 10.1016/S0022-2836(02)00194-8  0.665
2002 Banavali NK, Im W, Roux B. Electrostatic free energy calculations using the generalized solvent boundary potential method The Journal of Chemical Physics. 117: 7381-7388. DOI: 10.1063/1.1507108  0.321
2001 Marquez VE, Wang P, Nicklaus MC, Maier M, Manoharan M, Christman JK, Banavali NK, Mackerell AD. Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites. Nucleosides, Nucleotides & Nucleic Acids. 20: 451-9. PMID 11563060 DOI: 10.1081/Ncn-100002319  0.601
2001 Banavali NK, MacKerell AD. Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA. Nucleic Acids Research. 29: 3219-30. PMID 11470880 DOI: 10.1093/Nar/29.15.3219  0.614
2001 Banavali NK, MacKerell AD. Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3'-phosphoramidate moieties of nucleic acids. Journal of the American Chemical Society. 123: 6747-55. PMID 11448177 DOI: 10.1021/JA010295W  0.508
2000 MacKerell AD, Banavali N, Foloppe N. Development and current status of the CHARMM force field for nucleic acids Biopolymers. 56: 257-265. PMID 11754339 DOI: 10.1002/1097-0282(2000)56:4<257::Aid-Bip10029>3.0.Co;2-W  0.337
2000 Wang P, Brank AS, Banavali NK, Nicklaus MC, Marquez VE, Christman JK, Mackerell JD. Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by hhaI DNA (cytosine C5)-methyltransferase Journal of the American Chemical Society. 122: 12422-12434. DOI: 10.1021/Ja001989S  0.468
2000 MacKerell AD, Banavali NK. All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution Journal of Computational Chemistry. 21: 105-120. DOI: 10.1002/(Sici)1096-987X(20000130)21:2<105::Aid-Jcc3>3.0.Co;2-P  0.519
1996 Wang P, Denoya CD, Morgenstern MR, Skinner DD, Wallace KK, Digate R, Patton S, Banavali N, Schuler G, Speedie MK, Reynolds KA. Cloning and characterization of the gene encoding 1- cyclohexenylcarbonyl coenzyme A reductase from Streptomyces collinus Journal of Bacteriology. 178: 6873-6881. PMID 8955309 DOI: 10.1128/Jb.178.23.6873-6881.1996  0.313
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