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. RNA folding using quantum computers. PLoS Comput Biol. 2022 04; 18(4):e1010032. Fox DM, MacDermaid CM, Schreij AMA, Zwierzyna M, Walker RC. PMID: 35404931; PMCID: PMC9022793.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    2. Lipid21: Complex Lipid Membrane Simulations with AMBER. J Chem Theory Comput. 2022 Mar 08; 18(3):1726-1736. Dickson CJ, Walker RC, Gould IR. PMID: 35113553; PMCID: PMC9007451.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    3. 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; PMCID: PMC6995774.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    4. 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; PMCID: PMC6456390.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    5. 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; PMCID: PMC6476308.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    6. 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; PMCID: PMC6226240.
      View in: PubMed   Mentions: 112     Fields:    Translation:Cells
    7. 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: 27     Fields:    Translation:Cells
    8. 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; PMCID: PMC5915299.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    9. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 07 11; 114(28):7260-7265. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. PMID: 28652374; PMCID: PMC5514767.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    10. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophys J. 2017 Jun 20; 112(12):2469-2474. Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, Altintas I, Amaro RE. PMID: 28636905; PMCID: PMC5479118.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    11. 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. Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. PMID: 28470855.
      View in: PubMed   Mentions:    Fields:    
    12. 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. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. PMID: 27800559; PMCID: PMC5084073.
      View in: PubMed   Mentions: 51  
    13. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field. Data Brief. 2016 Sep; 8:1209-14. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. PMID: 27547799; PMCID: PMC4979044.
      View in: PubMed   Mentions: 5  
    14. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 08 05; 37(21):2029-37. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. PMID: 27317094; PMCID: PMC5052087.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    15. 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. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. PMID: 27317965; PMCID: PMC4995112.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    16. 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. Han Du WG, Götz AW, Yang L, Walker RC, Noodleman L. PMID: 27094074; PMCID: PMC4972664.
      View in: PubMed   Mentions: 13     Fields:    
    17. Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 2016 Apr 21; 18(15):10573-84. Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. PMID: 27034995; PMCID: PMC5091658.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    18. 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. Moonsamy S, Bhakat S, Walker RC, Soliman ME. PMID: 26972300.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    19. 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. Andersen OJ, Grouleff J, Needham P, Walker RC, Jensen F. PMID: 26482713.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. 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. Madej BD, Gould IR, Walker RC. PMID: 26359797; PMCID: PMC5079186.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    21. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. J Chem Theory Comput. 2015 Apr 14; 11(4):1864-74. Hopkins CW, Le Grand S, Walker RC, Roitberg AE. PMID: 26574392.
      View in: PubMed   Mentions: 332     Fields:    Translation:AnimalsCells
    22. All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb). 2015 Mar 14; 51(21):4402-5. Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. PMID: 25679020; PMCID: PMC5084445.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    23. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J. 2015 Mar 10; 108(5):1153-64. Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. PMID: 25762327; PMCID: PMC4375717.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    24. Adaptive mutations alter antibody structure and dynamics during affinity maturation. Biochemistry. 2015 Mar 24; 54(11):2085-93. Adhikary R, Yu W, Oda M, Walker RC, Chen T, Stanfield RL, Wilson IA, Zimmermann J, Romesberg FE. PMID: 25756188; PMCID: PMC5061043.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    25. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. J Comput Chem. 2015 Apr 05; 36(9):633-48. Mones L, Jones A, Götz AW, Laino T, Walker RC, Leimkuhler B, Csányi G, Bernstein N. PMID: 25649827; PMCID: PMC4351341.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    26. Paramfit: automated optimization of force field parameters for molecular dynamics simulations. J Comput Chem. 2015 Jan 15; 36(2):79-87. Betz RM, Walker RC. PMID: 25413259.
      View in: PubMed   Mentions: 20     Fields:    
    27. 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. Noodleman L, Han Du WG, Fee JA, Götz AW, Walker RC. PMID: 24960612; PMCID: PMC4095914.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    28. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput. 2014 Aug 12; 10(8):3473-3483. Zhang X, Walker RC, Phizicky EM, Mathews DH. PMID: 25136272; PMCID: PMC4132867.
      View in: PubMed   Mentions: 12     Fields:    
    29. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. J Chem Theory Comput. 2014 May 13; 10(5):2185-93. Mendieta-Moreno JI, Walker RC, Lewis JP, Gómez-Puertas P, Mendieta J, Ortega J. PMID: 26580543.
      View in: PubMed   Mentions: 6     Fields:    
    30. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08; 10(7):2677-2689. Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. PMID: 25061441; PMCID: PMC4095935.
      View in: PubMed   Mentions: 126     Fields:    
    31. Immunoglobulin G1 Fc domain motions: implications for Fc engineering. J Mol Biol. 2014 Apr 17; 426(8):1799-811. Frank M, Walker RC, Lanzilotta WN, Prestegard JH, Barb AW. PMID: 24522230; PMCID: PMC4041121.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    32. Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 2014 Feb 11; 10(2):865-879. Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC. PMID: 24803855; PMCID: PMC3985482.
      View in: PubMed   Mentions: 362     Fields:    
    33. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem. 2014 Jan 15; 35(2):95-108. Götz AW, Clark MA, Walker RC. PMID: 24122798; PMCID: PMC4063945.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    34. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package. J Chem Theory Comput. 2013 Sep 10; 9(9). Kaus JW, Pierce LT, Walker RC, McCammont JA. PMID: 24185531; PMCID: PMC3811123.
      View in: PubMed   Mentions: 32     Fields:    
    35. Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol. 2013; 9(9):e1003188. Barkho S, Pierce LC, McGlone ML, Li S, Woods VL, Walker RC, Adams JA, Jennings PA. PMID: 24039559; PMCID: PMC3764022.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    36. 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. Bastidas AC, Pierce LC, Walker RC, Johnson DA, Taylor SS. PMID: 24003983; PMCID: PMC3788587.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    37. 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. Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC. PMID: 26592383.
      View in: PubMed   Mentions: 922     Fields:    
    38. 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. Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. PMID: 23476156; PMCID: PMC3590007.
      View in: PubMed   Mentions: 24     Fields:    
    39. LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B. 2012 Sep 13; 116(36):11124-36. Skjevik ÅA, Madej BD, Walker RC, Teigen K. PMID: 22916730; PMCID: PMC3771533.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    40. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput. 2012 Sep 11; 8(9):2997-3002. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. PMID: 22984356; PMCID: PMC3438784.
      View in: PubMed   Mentions: 180     Fields:    
    41. Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems. J Chem Theory Comput. 2012 Aug 14; 8(8):2868-77. Park K, Götz AW, Walker RC, Paesani F. PMID: 26592126.
      View in: PubMed   Mentions: 15     Fields:    
    42. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. PMID: 22872804; PMCID: PMC3410406.
      View in: PubMed   Mentions: 2  
    43. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput. 2012 May 08; 8(5):1542-1555. Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. PMID: 22582031; PMCID: PMC3348677.
      View in: PubMed   Mentions: 597     Fields:    
    44. Carbinolamine formation and dehydration in a DNA repair enzyme active site. PLoS One. 2012; 7(2):e31377. Dodson ML, Walker RC, Lloyd RS. PMID: 22384015; PMCID: PMC3285167.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    45. A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol. 2012; 857:137-73. Nurisso A, Daina A, Walker RC. PMID: 22323220.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    46. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. PMID: 21750542; PMCID: PMC3144582.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    47. 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: 14     Fields:    
    48. 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: 113     Fields:    
    49. 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; PMCID: PMC3197852.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    50. 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: 11     Fields:    Translation:AnimalsCells
    51. 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:    
    52. 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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