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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.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
7 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
16 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
4 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
112 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
27 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
19 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
68 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
9 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions:
51
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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.
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PubMed Mentions:
5
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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.
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PubMed Mentions:
41 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
13 Fields:
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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.
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PubMed Mentions:
11 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
18 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
332 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
19 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
55 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
18 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
20 Fields:
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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.
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PubMed Mentions:
19 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
12 Fields:
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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.
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PubMed Mentions:
6 Fields:
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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.
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PubMed Mentions:
126 Fields:
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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.
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PubMed Mentions:
40 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
362 Fields:
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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.
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PubMed Mentions:
38 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
32 Fields:
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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.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
10 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
922 Fields:
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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.
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PubMed Mentions:
24 Fields:
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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.
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PubMed Mentions:
50 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
180 Fields:
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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.
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PubMed Mentions:
15 Fields:
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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.
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PubMed Mentions:
2
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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.
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PubMed Mentions:
597 Fields:
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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.
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PubMed Mentions: Fields:
Translation:
Cells
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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.
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PubMed Mentions:
7 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
54 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
14 Fields:
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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.
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PubMed Mentions:
113 Fields:
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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.
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PubMed Mentions:
60 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
11 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
6 Fields:
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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