Onufriev A - Search Results

1

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.

Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL 3rd. Feig M, et al. Among authors: onufriev a. J Comput Chem. 2004 Jan 30;25(2):265-84. doi: 10.1002/jcc.10378. J Comput Chem. 2004. PMID: 14648625

2

Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.

Onufriev AV. Onufriev AV. Front Mol Biosci. 2023 Apr 18;10:1067787. doi: 10.3389/fmolb.2023.1067787. eCollection 2023. Front Mol Biosci. 2023. PMID: 37143824 Free PMC article.

3

Correction to "Fast Polarizable Water Model for Atomistic Simulations".

Xiong Y, Izadi S, Onufriev AV. Xiong Y, et al. Among authors: onufriev av. J Chem Theory Comput. 2023 Jan 10;19(1):377. doi: 10.1021/acs.jctc.2c01188. Epub 2022 Dec 23. J Chem Theory Comput. 2023. PMID: 36563031 No abstract available.

4

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment.

Kolesnikov ES, Gushchin IY, Zhilyaev PA, Onufriev AV. Kolesnikov ES, et al. Among authors: onufriev av. J Chem Phys. 2023 Oct 14;159(14):145103. doi: 10.1063/5.0159341. J Chem Phys. 2023. PMID: 37815107

5

A novel view of pH titration in biomolecules.

Onufriev A, Case DA, Ullmann GM. Onufriev A, et al. Biochemistry. 2001 Mar 27;40(12):3413-9. doi: 10.1021/bi002740q. Biochemistry. 2001. PMID: 11297406

6

Effective Born radii in the generalized Born approximation: the importance of being perfect.

Onufriev A, Case DA, Bashford D. Onufriev A, et al. J Comput Chem. 2002 Nov 15;23(14):1297-304. doi: 10.1002/jcc.10126. J Comput Chem. 2002. PMID: 12214312

7

Structural details, pathways, and energetics of unfolding apomyoglobin.

Onufriev A, Case DA, Bashford D. Onufriev A, et al. J Mol Biol. 2003 Jan 17;325(3):555-67. doi: 10.1016/s0022-2836(02)01207-x. J Mol Biol. 2003. PMID: 12498802

8

Modeling of flap endonuclease interactions with DNA substrate.

Allawi HT, Kaiser MW, Onufriev AV, Ma WP, Brogaard AE, Case DA, Neri BP, Lyamichev VI. Allawi HT, et al. Among authors: onufriev av. J Mol Biol. 2003 May 2;328(3):537-54. doi: 10.1016/s0022-2836(03)00351-6. J Mol Biol. 2003. PMID: 12706715

9

Exploring protein native states and large-scale conformational changes with a modified generalized born model.

Onufriev A, Bashford D, Case DA. Onufriev A, et al. Proteins. 2004 May 1;55(2):383-94. doi: 10.1002/prot.20033. Proteins. 2004. PMID: 15048829

10

The Amber biomolecular simulation programs.

Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. Case DA, et al. Among authors: onufriev a. J Comput Chem. 2005 Dec;26(16):1668-88. doi: 10.1002/jcc.20290. J Comput Chem. 2005. PMID: 16200636 Free PMC article.

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