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230 results
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Automatic atom type and bond type perception in molecular mechanical calculations.
Wang J, Wang W, Kollman PA, Case DA. Wang J, et al. Among authors: case da. J Mol Graph Model. 2006 Oct;25(2):247-60. doi: 10.1016/j.jmgm.2005.12.005. Epub 2006 Feb 3. J Mol Graph Model. 2006. PMID: 16458552
NMR structure of a cyclic polyamide-DNA complex.
Zhang Q, Dwyer TJ, Tsui V, Case DA, Cho J, Dervan PB, Wemmer DE. Zhang Q, et al. Among authors: case da. J Am Chem Soc. 2004 Jun 30;126(25):7958-66. doi: 10.1021/ja0373622. J Am Chem Soc. 2004. PMID: 15212545
All-atom crystal simulations of DNA and RNA duplexes.
Liu C, Janowski PA, Case DA. Liu C, et al. Among authors: case da. Biochim Biophys Acta. 2015 May;1850(5):1059-1071. doi: 10.1016/j.bbagen.2014.09.018. Epub 2014 Sep 26. Biochim Biophys Acta. 2015. PMID: 25255706 Free PMC article.
Development and testing of a general amber force field.
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Wang J, et al. Among authors: case da. J Comput Chem. 2004 Jul 15;25(9):1157-74. doi: 10.1002/jcc.20035. J Comput Chem. 2004. PMID: 15116359
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods.
Gouda H, Kuntz ID, Case DA, Kollman PA. Gouda H, et al. Among authors: case da. Biopolymers. 2003 Jan;68(1):16-34. doi: 10.1002/bip.10270. Biopolymers. 2003. PMID: 12579577
Continuum solvent molecular dynamics study of flexibility in interleukin-8.
Cornell W, Abseher R, Nilges M, Case DA. Cornell W, et al. Among authors: case da. J Mol Graph Model. 2001;19(1):136-45. doi: 10.1016/s1093-3263(00)00124-8. J Mol Graph Model. 2001. PMID: 11381524
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd. Kollman PA, et al. Among authors: case da. Acc Chem Res. 2000 Dec;33(12):889-97. doi: 10.1021/ar000033j. Acc Chem Res. 2000. PMID: 11123888
Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Graves AP, et al. Among authors: case da. J Mol Biol. 2008 Mar 28;377(3):914-34. doi: 10.1016/j.jmb.2008.01.049. Epub 2008 Jan 30. J Mol Biol. 2008. PMID: 18280498 Free PMC article.
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.
Mathews DH, Case DA. Mathews DH, et al. Among authors: case da. J Mol Biol. 2006 Apr 14;357(5):1683-93. doi: 10.1016/j.jmb.2006.01.054. Epub 2006 Feb 3. J Mol Biol. 2006. PMID: 16487974
DOCK 6: combining techniques to model RNA-small molecule complexes.
Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. Lang PT, et al. Among authors: case da. RNA. 2009 Jun;15(6):1219-30. doi: 10.1261/rna.1563609. Epub 2009 Apr 15. RNA. 2009. PMID: 19369428 Free PMC article.
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