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Ross Walker

Title(s)Associate Adjunct Professor, Chemistry and Biochemistry
SchoolVc-academic Affairs
Address9500 Gilman Drive #
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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. X-ray Crystallographic and Molecular Dynamic Analyses of Drosophila melanogaster Embryonic Muscle Myosin Define Domains Responsible for Isoform-Specific Properties. J Mol Biol. 2020 01 17; 432(2):427-447. Caldwell JT, Mermelstein DJ, Walker RC, Bernstein SI, Huxford T. PMID: 31786266.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    2. Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 2019 Apr 09; 15(4):2684-2691. Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. PMID: 30835999.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    3. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit. 2019 03; 32(3):e2765. Mermelstein DJ, McCammon JA, Walker RC. PMID: 30264484.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    4. GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model. 2018 10 22; 58(10):2043-2050. Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. PMID: 30199633.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    5. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 2018 07 15; 39(19):1354-1358. Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. PMID: 29532496.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    6. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. 2018 03 06; 57(9):1533-1541. Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. PMID: 29394043.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    7. 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   Mentions: 19     Fields:    Translation:Cells
    8. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophys J. 2017 Jun 20; 112(12):2469-2474. PMID: 28636905.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    9. 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 07 05; 38(18):1631-1639. PMID: 28470855.
      View in: PubMed   Mentions:    Fields:    
    10. 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   Mentions:
    11. 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.
      View in: PubMed   Mentions:
    12. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 08 05; 37(21):2029-37. PMID: 27317094.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    13. 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   Mentions: 6     Fields:    Translation:Cells
    14. 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.
      View in: PubMed   Mentions: 9     Fields:    
    15. 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   Mentions: 3     Fields:    Translation:Cells
    16. 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   Mentions: 1     Fields:    Translation:Cells
    17. 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   Mentions: 2     Fields:    Translation:Cells
    18. 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   Mentions: 9     Fields:    Translation:Cells
    19. 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   Mentions: 113     Fields:    Translation:AnimalsCells
    20. 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   Mentions: 10     Fields:    Translation:Cells
    21. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J. 2015 Mar 10; 108(5):1153-64. PMID: 25762327.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    22. Adaptive mutations alter antibody structure and dynamics during affinity maturation. Biochemistry. 2015 Mar 24; 54(11):2085-93. PMID: 25756188.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    23. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    24. 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   Mentions: 9     Fields:    
    25. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    26. 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   Mentions: 7     Fields:    
    27. 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   Mentions: 2     Fields:    
    28. 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   Mentions: 56     Fields:    
    29. Immunoglobulin G1 Fc domain motions: implications for Fc engineering. J Mol Biol. 2014 Apr 17; 426(8):1799-811. PMID: 24522230.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    30. Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 2014 Feb 11; 10(2):865-879. PMID: 24803855.
      View in: PubMed   Mentions: 151     Fields:    
    31. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem. 2014 Jan 15; 35(2):95-108. PMID: 24122798.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    32. 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   Mentions: 25     Fields:    
    33. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    34. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    35. 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   Mentions: 419     Fields:    
    36. 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   Mentions: 9     Fields:    
    37. LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B. 2012 Sep 13; 116(36):11124-36. PMID: 22916730.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    38. 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   Mentions: 99     Fields:    
    39. 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   Mentions: 14     Fields:    
    40. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. PMID: 22872804.
      View in: PubMed   Mentions:
    41. 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   Mentions: 320     Fields:    
    42. Carbinolamine formation and dehydration in a DNA repair enzyme active site. PLoS One. 2012; 7(2):e31377. PMID: 22384015.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    43. A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol. 2012; 857:137-73. PMID: 22323220.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    44. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. PMID: 21750542.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    45. 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. Sherrill CD, Sumpter BG, Sinnokrot MO, Marshall MS, Hohenstein EG, Walker RC, Gould IR. PMID: 19242959.
      View in: PubMed   Mentions: 10     Fields:    
    46. The implementation of a fast and accurate QM/MM potential method in Amber. J Comput Chem. 2008 May; 29(7):1019-31. Walker RC, Crowley MF, Case DA. PMID: 18072177.
      View in: PubMed   Mentions: 67     Fields:    
    47. 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. de M Seabra G, Walker RC, Elstner M, Case DA, Roitberg AE. PMID: 17521173.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    48. Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface. Protein Eng Des Sel. 2007 Apr; 20(4):179-87. Nimlos MR, Matthews JF, Crowley MF, Walker RC, Chukkapalli G, Brady JW, Adney WS, Cleary JM, Zhong L, Himmel ME. PMID: 17430975.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    49. 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. Walker RC, Mercer IP, Gould IR, Klug DR. PMID: 17186476.
      View in: PubMed   Mentions: 6     Fields:    
    50. Effect of adiabaticity on electron dynamics in zinc myoglobin. J Phys Chem B. 2005 Mar 31; 109(12):5954-61. Cho BM, Walker RC, Amer H, Mercer I, Klug DR, Gould IR. PMID: 16851650.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
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