Xiaolin Cheng, Ph.D. - Publications

Affiliations: 
2004 Stony Brook University, Stony Brook, NY, United States 

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Mostofian B, Cai CM, Smith MD, Petridis L, Cheng X, Wyman CE, Smith JC. Local Phase Separation of Co-Solvents Enhances Pretreatment of Biomass for Bioenergy Applications. Journal of the American Chemical Society. PMID 27482599 DOI: 10.1021/jacs.6b03285  0.76
2016 Tian J, Nickels JD, Katsaras J, Cheng X. The Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies. The Journal of Physical Chemistry. B. PMID 27121138 DOI: 10.1021/acs.jpcb.6b02148  0.76
2015 Chen Q, Luan ZJ, Yu HL, Cheng X, Xu JH. Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding. Journal of Molecular Graphics & Modelling. 62: 319-324. PMID 26556053 DOI: 10.1016/j.jmgm.2015.10.015  0.76
2015 Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DA, Ohl M, Katsaras J. Mechanical properties of nanoscopic lipid domains. Journal of the American Chemical Society. PMID 26415030 DOI: 10.1021/jacs.5b08894  0.76
2015 Khadka NK, Cheng X, Ho CS, Katsaras J, Pan J. Interactions of the anticancer drug tamoxifen with lipid membranes. Biophysical Journal. 108: 2492-501. PMID 25992727 DOI: 10.1016/j.bpj.2015.04.010  0.76
2015 Wall JS, Martin EB, Richey T, Stuckey AC, Macy S, Wooliver C, Williams A, Foster JS, McWilliams-Koeppen P, Uberbacher E, Cheng X, Kennel SJ. Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis. Molecules (Basel, Switzerland). 20: 7657-82. PMID 25923515 DOI: 10.3390/molecules20057657  0.76
2015 Chen Q, Luan ZJ, Cheng X, Xu JH. Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase. Biochemistry. 54: 1841-8. PMID 25711934 DOI: 10.1021/bi5015612  0.76
2015 Chen Q, Cheng X, Wei D, Xu Q. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase. Interdisciplinary Sciences, Computational Life Sciences. 7: 36-42. PMID 25519157 DOI: 10.1007/s12539-014-0235-8  0.76
2015 Nickels JD, Smith JC, Cheng X. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes Chemistry and Physics of Lipids. DOI: 10.1016/j.chemphyslip.2015.07.012  0.76
2014 Mostofian B, Cheng X, Smith JC. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. The Journal of Physical Chemistry. B. 118: 11037-49. PMID 25180945 DOI: 10.1021/jp502889c  0.76
2014 Hong L, Sharp MA, Poblete S, Biehl R, Zamponi M, Szekely N, Appavou MS, Winkler RG, Nauss RE, Johs A, Parks JM, Yi Z, Cheng X, Liang L, Ohl M, et al. Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophysical Journal. 107: 393-400. PMID 25028881 DOI: 10.1016/j.bpj.2014.06.013  0.76
2014 Pan J, Cheng X, Monticelli L, Heberle FA, Kučerka N, Tieleman DP, Katsaras J. The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations. Soft Matter. 10: 3716-25. PMID 24807693 DOI: 10.1039/c4sm00066h  0.76
2014 Le RK, Harris BJ, Iwuchukwu IJ, Bruce BD, Cheng X, Qian S, Heller WT, O'Neill H, Frymier PD. Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-D-maltoside using small-angle neutron scattering and molecular dynamics simulation. Archives of Biochemistry and Biophysics. 550: 50-7. PMID 24769336 DOI: 10.1016/j.abb.2014.04.005  0.76
2014 Srinivas G, Cheng X, Smith JC. Coarse-grain model for natural cellulose fibrils in explicit water. The Journal of Physical Chemistry. B. 118: 3026-34. PMID 24564237 DOI: 10.1021/jp407953p  0.76
2014 Harris BJ, Cheng X, Frymier P. All-atom molecular dynamics simulation of a photosystem I/detergent complex Journal of Physical Chemistry B. 118: 11633-11645. DOI: 10.1021/jp507157e  0.76
2014 Alekozai EM, GhattyVenkataKrishna PK, Uberbacher EC, Crowley MF, Smith JC, Cheng X. Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ Cellulose. 21: 951-971. DOI: 10.1007/s10570-013-0026-0  0.76
2014 Mostofian B, Smith JC, Cheng X. Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution Cellulose. 21: 983-997. DOI: 10.1007/s10570-013-0018-0  0.76
2013 Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, Wei D. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. Journal of Chemical Information and Modeling. 53: 3297-307. PMID 24205814 DOI: 10.1021/ci400537n  0.76
2013 Sharma H, Sanchez TW, Neamati N, Detorio M, Schinazi RF, Cheng X, Buolamwini JK. Synthesis, docking, and biological studies of phenanthrene β-diketo acids as novel HIV-1 integrase inhibitors. Bioorganic & Medicinal Chemistry Letters. 23: 6146-51. PMID 24091080 DOI: 10.1016/j.bmcl.2013.09.009  0.76
2013 Wang X, Yang T, Cheng X, Shen Q. Enantioselective electrophilic trifluoromethylthiolation of β-ketoesters: a case of reactivity and selectivity bias for organocatalysis. Angewandte Chemie (International Ed. in English). 52: 12860-4. PMID 24000200 DOI: 10.1002/anie.201305075  0.76
2013 Devarajan A, Markutsya S, Lamm MH, Cheng X, Smith JC, Baluyut JY, Kholod Y, Gordon MS, Windus TL. Ab initio study of molecular interactions in cellulose Iα. The Journal of Physical Chemistry. B. 117: 10430-43. PMID 23937275 DOI: 10.1021/jp406266u  0.76
2013 GhattyVenkataKrishna PK, Uberbacher EC, Cheng X. Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates. Febs Letters. 587: 2649-55. PMID 23845280 DOI: 10.1016/j.febslet.2013.06.050  0.76
2013 Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity. Biophysical Journal. 104: 904-12. PMID 23442969 DOI: 10.1016/j.bpj.2012.12.052  0.76
2013 Zhang B, Lu B, Cheng X, Huang J, Pitsianis NP, Sun X, McCammon JA. Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver Communications in Computational Physics. 13: 107-128. DOI: 10.4208/cicp.210711.111111s  0.76
2013 Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems Computer Physics Communications. 184: 2618-2619. DOI: 10.1016/j.cpc.2013.05.012  0.76
2012 Pan J, Cheng X, Heberle FA, Mostofian B, Kučerka N, Drazba P, Katsaras J. Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations. The Journal of Physical Chemistry. B. 116: 14829-38. PMID 23199292 DOI: 10.1021/jp310345j  0.76
2012 Cheng X, Ivanov I. Molecular dynamics. Methods in Molecular Biology (Clifton, N.J.). 929: 243-85. PMID 23007433 DOI: 10.1007/978-1-62703-050-2_11  0.76
2012 Hong L, Cheng X, Glass DC, Smith JC. Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Physical Review Letters. 108: 238102. PMID 23003993 DOI: 10.1103/PhysRevLett.108.238102  0.76
2012 Glass DC, Moritsugu K, Cheng X, Smith JC. REACH coarse-grained simulation of a cellulose fiber. Biomacromolecules. 13: 2634-44. PMID 22937726 DOI: 10.1021/bm300460f  0.76
2012 Sharma H, Cheng X, Buolamwini JK. Homology model-guided 3D-QSAR studies of HIV-1 integrase inhibitors. Journal of Chemical Information and Modeling. 52: 515-44. PMID 22256860 DOI: 10.1021/ci200485a  0.76
2012 Wang HL, Cheng X, Sine SM. Intramembrane proton binding site linked to activation of bacterial pentameric ion channel. The Journal of Biological Chemistry. 287: 6482-9. PMID 22084238 DOI: 10.1074/jbc.M111.305839  0.76
2012 Cheng X, Parks JM, Petridis L, Lindner B, Schulz R, Guo HB, Srinivas G, Smith JC. Molecular simulation in the energy biosciences Rsc Biomolecular Sciences. 1: 87-114.  0.76
2011 Srinivas G, Cheng X, Smith JC. A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils. Journal of Chemical Theory and Computation. 7: 2539-48. PMID 26606627 DOI: 10.1021/ct200181t  0.76
2011 Xu Z, Cai W, Cheng X. Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model. Communications in Computational Physics. 9: 1056-1070. PMID 23504509 DOI: 10.4208/cicp.160410.200910a  0.76
2011 Mostofian B, Smith JC, Cheng X. The solvation structures of cellulose microfibrils in ionic liquids. Interdisciplinary Sciences, Computational Life Sciences. 3: 308-20. PMID 22179764 DOI: 10.1007/s12539-011-0111-8  0.76
2011 Cheng X, Xu Z. Editorial: special issue on ionic fluids and its biological application. Interdisciplinary Sciences, Computational Life Sciences. 3: 241-2. PMID 22179757 DOI: 10.1007/s12539-011-0112-7  0.76
2011 Klein HC, Cheng X, Smith JC, Shen T. Transfer matrix approach to the hydrogen-bonding in cellulose Iα fibrils describes the recalcitrance to thermal deconstruction. The Journal of Chemical Physics. 135: 085106. PMID 21895224 DOI: 10.1063/1.3626274  0.76
2011 Xu Z, Cheng X, Yang H. Treecode-based generalized Born method. The Journal of Chemical Physics. 134: 064107. PMID 21322661 DOI: 10.1063/1.3552945  0.76
2011 Fritsch S, Ivanov I, Wang H, Cheng X. Ion selectivity mechanism in a bacterial pentameric ligand-gated ion channel. Biophysical Journal. 100: 390-8. PMID 21244835 DOI: 10.1016/j.bpj.2010.11.077  0.76
2010 Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Computer Physics Communications. 181: 1150-1160. PMID 20532187 DOI: 10.1016/j.cpc.2010.02.015  0.76
2010 Petridis L, Xu J, Crowley MF, Smith JC, Cheng X. Atomistic simulation of lignocellulosic biomass and associated cellulosomal protein complexes Acs Symposium Series. 1052: 55-73. DOI: 10.1021/bk-2010-1052.ch003  0.76
2009 Lu B, Cheng X, Huang J, McCammon JA. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. Journal of Chemical Theory and Computation. 5: 1692-1699. PMID 19517026 DOI: 10.1021/ct900083k  0.76
2009 Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophysical Journal. 96: 4502-13. PMID 19486673 DOI: 10.1016/j.bpj.2009.03.018  0.76
2009 Wang HL, Toghraee R, Papke D, Cheng XL, McCammon JA, Ravaioli U, Sine SM. Single-channel current through nicotinic receptor produced by closure of binding site C-loop. Biophysical Journal. 96: 3582-90. PMID 19413963 DOI: 10.1016/j.bpj.2009.02.020  0.76
2009 Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. Journal of the American Chemical Society. 131: 4702-9. PMID 19296611 DOI: 10.1021/ja8085643  0.76
2008 Cheng YH, Cheng XL, Radić Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chemico-Biological Interactions. 175: 196-9. PMID 18657802 DOI: 10.1016/j.cbi.2008.04.044  0.76
2008 Wang HL, Cheng X, Taylor P, McCammon JA, Sine SM. Control of cation permeation through the nicotinic receptor channel. Plos Computational Biology. 4: e41. PMID 18282090 DOI: 10.1371/journal.pcbi.0040041  0.76
2007 Lu B, Cheng X, McCammon JA. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. Journal of Computational Physics. 226: 1348-1366. PMID 18379638 DOI: 10.1016/j.jcp.2007.05.026  0.76
2007 Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophysical Journal. 93: 2622-34. PMID 17573436 DOI: 10.1529/biophysj.107.109843  0.76
2007 Ivanov I, Cheng X, Sine SM, McCammon JA. Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. Journal of the American Chemical Society. 129: 8217-24. PMID 17552523 DOI: 10.1021/ja070778l  0.76
2007 Cheng Y, Cheng X, Radić Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. Journal of the American Chemical Society. 129: 6562-70. PMID 17461584 DOI: 10.1021/ja070601r  0.76
2006 Lu B, Cheng X, Huang J, McCammon JA. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proceedings of the National Academy of Sciences of the United States of America. 103: 19314-9. PMID 17148613 DOI: 10.1073/pnas.0605166103  0.76
2006 Cheng X, Wang H, Grant B, Sine SM, McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. Plos Computational Biology. 2: e134. PMID 17009865 DOI: 10.1371/journal.pcbi.0020134  0.76
2006 Rafi SB, Cui G, Song K, Cheng X, Tonge PJ, Simmerling C. Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase. Journal of Medicinal Chemistry. 49: 4574-80. PMID 16854062 DOI: 10.1021/jm060222t  0.76
2006 Cheng X, Lu B, Grant B, Law RJ, McCammon JA. Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. Journal of Molecular Biology. 355: 310-24. PMID 16307758 DOI: 10.1016/j.jmb.2005.10.039  0.76
2005 Cheng X, Cui G, Hornak V, Simmerling C. Modified replica exchange simulation methods for local structure refinement. The Journal of Physical Chemistry. B. 109: 8220-30. PMID 16851961 DOI: 10.1021/jp045437y  0.76
2005 Cheng X, Kelso C, Hornak V, de los Santos C, Grollman AP, Simmerling C. Dynamic behavior of DNA base pairs containing 8-oxoguanine. Journal of the American Chemical Society. 127: 13906-18. PMID 16201812 DOI: 10.1021/ja052542s  0.76
2005 Lu B, Cheng X, Hou T, McCammon JA. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. The Journal of Chemical Physics. 123: 084904. PMID 16164327 DOI: 10.1063/1.2008252  0.76
2004 Cheng X, Hornak V, Simmerling C. Improved conformational sampling through an efficient combination of mean-field simulation approaches Journal of Physical Chemistry B. 108: 426-437.  0.76
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