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Ross Walker

TitleAssociate Adjunct Professor
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0332
La Jolla CA 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. Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit. 2018 Sep 27; e2765. PMID: 30264484.
      View in: PubMed
    2. Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg AE, Case DA, Walker RC, York DM. GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. J Chem Inf Model. 2018 Sep 10. PMID: 30199633.
      View in: PubMed
    3. Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 2018 Mar 12. PMID: 29532496.
      View in: PubMed
    4. Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. 2018 03 06; 57(9):1533-1541. PMID: 29394043.
      View in: PubMed
    5. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 07 11; 114(28):7260-7265. PMID: 28652374.
      View in: PubMed
    6. Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, 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
    7. Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. J Comput Chem. 2017 Jul 05; 38(18):1631-1639. PMID: 28470855.
      View in: PubMed
    8. Palermo G, Miao Y, Walker RC, 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
    9. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, 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.
    10. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, 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
    11. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, 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):1594-1606. PMID: 27317965.
      View in: PubMed
    12. Han Du WG, Götz AW, Yang L, Walker RC, 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].
    13. Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, 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
    14. Moonsamy S, Bhakat S, Walker RC, 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
    15. Andersen OJ, Grouleff J, Needham P, Walker RC, 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.
      View in: PubMed
    16. Madej BD, Gould IR, Walker RC. 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
    17. Hopkins CW, Le Grand S, Walker RC, Roitberg AE. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. J Chem Theory Comput. 2015 Apr 14; 11(4):1864-74. PMID: 26574392.
      View in: PubMed
    18. Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, 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
    19. Adhikary R, Yu W, Oda M, Walker RC, 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
    20. Anandakrishnan R, Drozdetski A, Walker RC, 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.
    21. Mones L, Jones A, Götz AW, Laino T, Walker RC, 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.
    22. Betz RM, Walker RC. 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
    23. Noodleman L, Han Du WG, Fee JA, Götz AW, Walker RC. 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.
    24. Zhang X, Walker RC, 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.
      View in: PubMed
    25. Mendieta-Moreno JI, Walker RC, 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.
      View in: PubMed
    26. Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, 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
    27. Frank M, Walker RC, 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.
    28. Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC. Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 2014 Feb 11; 10(2):865-879. PMID: 24803855.
      View in: PubMed
    29. Götz AW, Clark MA, Walker RC. 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.
    30. Kaus JW, Pierce LT, Walker RC, 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
    31. Barkho S, Pierce LC, McGlone ML, Li S, Woods VL, Walker RC, 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.
    32. Bastidas AC, Pierce LC, Walker RC, 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.
    33. Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC. 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.
      View in: PubMed
    34. Isborn CM, Götz AW, Clark MA, Walker RC, 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.
      View in: PubMed
    35. Skjevik ÅA, Madej BD, Walker RC, 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.
    36. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. 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
    37. Park K, Götz AW, Walker RC, 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
    38. Votapka L, Demir O, Swift RV, Walker RC, 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.
    39. Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. 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
    40. Dodson ML, Walker RC, Lloyd RS. Carbinolamine formation and dehydration in a DNA repair enzyme active site. PLoS One. 2012; 7(2):e31377. PMID: 22384015; PMCID: PMC3285167.
    41. Nurisso A, Daina A, Walker RC. A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol. 2012; 857:137-73. PMID: 22323220.
      View in: PubMed
    42. Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. PMID: 21750542; PMCID: PMC3144582.
    43. Sherrill CD, Sumpter BG, Sinnokrot MO, Marshall MS, Hohenstein EG, Walker RC, 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.
      View in: PubMed
    44. Walker RC, 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.
      View in: PubMed
    45. de M Seabra G, Walker RC, 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.
    46. Walker RC, 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.
      View in: PubMed
    47. Cho BM, Walker RC, 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