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    Ross Walker

    TitleAssociate Adjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentChemistry and Biochemistry
    Address9500 Gilman Drive #0332
    CA La Jolla 92093
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Palermo G, Miao Y, Walker R, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 Jul 11; 114(28):7260-7265. PMID: 28652374.
        View in: PubMed
      2. Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker R, Altintas I, Amaro RE. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophys J. 2017 Jun 20; 112(12):2469-2474. PMID: 28636905.
        View in: PubMed
      3. Palermo G, Miao Y, Walker R, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Cent Sci. 2016 Oct 26; 2(10):756-763. PMID: 27800559.
        View in: PubMed
      4. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker R, Götz AW. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field. Data Brief. 2016 Sep; 8:1209-14. PMID: 27547799; PMCID: PMC4979044.
      5. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker R, Gilson MK, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 Aug 05; 37(21):2029-37. PMID: 27317094.
        View in: PubMed
      6. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker R, Götz AW. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. Biochim Biophys Acta. 2016 09; 1857(9):1594-606. PMID: 27317965; PMCID: PMC4995112 [Available on 09/01/17].
      7. Han Du WG, Götz AW, Yang L, Walker R, Noodleman L. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus. Phys Chem Chem Phys. 2016 Aug 21; 18(31):21162-71. PMID: 27094074; PMCID: PMC4972664 [Available on 08/21/17].
      8. Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker R, Gould IR. Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 2016 Apr 21; 18(15):10573-84. PMID: 27034995.
        View in: PubMed
      9. Moonsamy S, Bhakat S, Walker R, Soliman ME. Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations. Cell Biochem Biophys. 2016 Mar; 74(1):35-48. PMID: 26972300.
        View in: PubMed
      10. Andersen OJ, Grouleff J, Needham P, Walker R, Jensen F. Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins. J Phys Chem B. 2015 Nov 19; 119(46):14594-603. PMID: 26482713.
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      11. Madej BD, Gould IR, Walker R. A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B. 2015 Sep 24; 119(38):12424-35. PMID: 26359797.
        View in: PubMed
      12. Hopkins CW, Le Grand S, Walker R, Roitberg AE. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. J Chem Theory Comput. 2015 Apr 14; 11(4):1864-74. PMID: 26574392.
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      13. Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker R, Gould IR. All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb). 2015 Mar 14; 51(21):4402-5. PMID: 25679020.
        View in: PubMed
      14. Adhikary R, Yu W, Oda M, Walker R, Chen T, Stanfield RL, Wilson IA, Zimmermann J, Romesberg FE. Adaptive mutations alter antibody structure and dynamics during affinity maturation. Biochemistry. 2015 Mar 24; 54(11):2085-93. PMID: 25756188.
        View in: PubMed
      15. Anandakrishnan R, Drozdetski A, Walker R, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J. 2015 Mar 10; 108(5):1153-64. PMID: 25762327; PMCID: PMC4375717.
      16. Mones L, Jones A, Götz AW, Laino T, Walker R, Leimkuhler B, Csányi G, Bernstein N. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. J Comput Chem. 2015 Apr 05; 36(9):633-48. PMID: 25649827; PMCID: PMC4351341.
      17. Betz RM, Walker R. Paramfit: automated optimization of force field parameters for molecular dynamics simulations. J Comput Chem. 2015 Jan 15; 36(2):79-87. PMID: 25413259.
        View in: PubMed
      18. Noodleman L, Han Du WG, Fee JA, Götz AW, Walker R. Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex. Inorg Chem. 2014 Jul 07; 53(13):6458-72. PMID: 24960612; PMCID: PMC4095914.
      19. Zhang X, Walker R, Phizicky EM, Mathews DH. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput. 2014 Aug 12; 10(8):3473-3483. PMID: 25136272.
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      20. Mendieta-Moreno JI, Walker R, Lewis JP, Gómez-Puertas P, Mendieta J, Ortega J. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. J Chem Theory Comput. 2014 May 13; 10(5):2185-93. PMID: 26580543.
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      21. Miao Y, Sinko W, Pierce L, Bucher D, Walker R, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08; 10(7):2677-2689. PMID: 25061441.
        View in: PubMed
      22. Frank M, Walker R, Lanzilotta WN, Prestegard JH, Barb AW. Immunoglobulin G1 Fc domain motions: implications for Fc engineering. J Mol Biol. 2014 Apr 17; 426(8):1799-811. PMID: 24522230; PMCID: PMC4041121.
      23. Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker R. Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 2014 Feb 11; 10(2):865-879. PMID: 24803855.
        View in: PubMed
      24. Götz AW, Clark MA, Walker R. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem. 2014 Jan 15; 35(2):95-108. PMID: 24122798; PMCID: PMC4063945.
      25. Kaus JW, Pierce LT, Walker R, McCammont JA. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package. J Chem Theory Comput. 2013 Sep 10; 9(9). PMID: 24185531.
        View in: PubMed
      26. Barkho S, Pierce LC, McGlone ML, Li S, Woods VL, Walker R, Adams JA, Jennings PA. Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol. 2013; 9(9):e1003188. PMID: 24039559; PMCID: PMC3764022.
      27. Bastidas AC, Pierce LC, Walker R, Johnson DA, Taylor SS. Influence of N-myristylation and ligand binding on the flexibility of the catalytic subunit of protein kinase A. Biochemistry. 2013 Sep 17; 52(37):6368-79. PMID: 24003983; PMCID: PMC3788587.
      28. Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker R. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. J Chem Theory Comput. 2013 Sep 10; 9(9):3878-88. PMID: 26592383.
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      29. Isborn CM, Götz AW, Clark MA, Walker R, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput. 2012 Dec 01; 8(12):5092-5106. PMID: 23476156.
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      30. Skjevik ÅA, Madej BD, Walker R, Teigen K. LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B. 2012 Sep 13; 116(36):11124-36. PMID: 22916730; PMCID: PMC3771533.
      31. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker R. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput. 2012 Sep 11; 8(9):2997-3002. PMID: 22984356.
        View in: PubMed
      32. Park K, Götz AW, Walker R, Paesani F. Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems. J Chem Theory Comput. 2012 Aug 14; 8(8):2868-77. PMID: 26592126.
        View in: PubMed
      33. Votapka L, Demir O, Swift RV, Walker R, Amaro RE. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. PMID: 22872804; PMCID: PMC3410406.
      34. Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker R. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput. 2012 May 08; 8(5):1542-1555. PMID: 22582031.
        View in: PubMed
      35. Dodson ML, Walker R, Lloyd RS. Carbinolamine formation and dehydration in a DNA repair enzyme active site. PLoS One. 2012; 7(2):e31377. PMID: 22384015; PMCID: PMC3285167.
      36. Nurisso A, Daina A, Walker R. A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol. 2012; 857:137-73. PMID: 22323220.
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      37. Amaro RE, Swift RV, Votapka L, Li WW, Walker R, Bush RM. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. PMID: 21750542; PMCID: PMC3144582.
      38. Sherrill CD, Sumpter BG, Sinnokrot MO, Marshall MS, Hohenstein EG, Walker R, Gould IR. Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions. J Comput Chem. 2009 Nov 15; 30(14):2187-93. PMID: 19242959.
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      39. Walker R, Crowley MF, Case DA. The implementation of a fast and accurate QM/MM potential method in Amber. J Comput Chem. 2008 May; 29(7):1019-31. PMID: 18072177.
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      40. de M Seabra G, Walker R, Elstner M, Case DA, Roitberg AE. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A. 2007 Jul 05; 111(26):5655-64. PMID: 17521173; PMCID: PMC3197852.
      41. Walker R, Mercer IP, Gould IR, Klug DR. Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations. J Comput Chem. 2007 Jan 30; 28(2):478-90. PMID: 17186476.
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      42. Cho BM, Walker R, Amer H, Mercer I, Klug DR, Gould IR. Effect of adiabaticity on electron dynamics in zinc myoglobin. J Phys Chem B. 2005 Mar 31; 109(12):5954-61. PMID: 16851650.
        View in: PubMed