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Items: 1 to 50 of 120

1.

A Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases.

Zong Z, Li Q, Hong Z, Fu H, Cai W, Chipot C, Jiang H, Zhang D, Chen S, Shao X.

J Am Chem Soc. 2019 Aug 21. doi: 10.1021/jacs.9b08477. [Epub ahead of print]

PMID:
31432675
2.

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual Topology Free Energy Perturbation Approach in NAMD.

Jiang W, Chipot C, Roux B.

J Chem Inf Model. 2019 Aug 14. doi: 10.1021/acs.jcim.9b00362. [Epub ahead of print]

PMID:
31411473
3.

Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features.

Oestringer BP, Bolivar JH, Claridge JK, Almanea L, Chipot C, Dehez F, Holzmann N, Schnell JR, Zitzmann N.

Sci Rep. 2019 Jun 10;9(1):8383. doi: 10.1038/s41598-019-44413-x.

4.

Binding properties of the quaternary assembly protein SPAG1.

Chagot ME, Dos Santos Morais R, Dermouche S, Lefebvre D, Manival X, Chipot C, Dehez F, Quinternet M.

Biochem J. 2019 Jun 14;476(11):1679-1694. doi: 10.1042/BCJ20190198.

PMID:
31118266
5.

Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane.

Tse CH, Comer J, Sang Chu SK, Wang Y, Chipot C.

J Chem Theory Comput. 2019 May 14;15(5):2913-2924. doi: 10.1021/acs.jctc.9b00022. Epub 2019 Apr 26.

PMID:
30998342
6.

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses.

Singharoy A, Chipot C, Ekimoto T, Suzuki K, Ikeguchi M, Yamato I, Murata T.

Front Physiol. 2019 Feb 5;10:46. doi: 10.3389/fphys.2019.00046. eCollection 2019. Review.

7.

Changes in Microenvironment Modulate the B- to A-DNA Transition.

Zhang H, Fu H, Shao X, Dehez F, Chipot C, Cai W.

J Chem Inf Model. 2019 May 28;59(5):2324-2330. doi: 10.1021/acs.jcim.8b00885. Epub 2019 Feb 28.

PMID:
30767527
8.

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water.

Lee H, Dehez F, Chipot C, Lim HK, Kim H.

J Chem Theory Comput. 2019 Mar 12;15(3):1538-1545. doi: 10.1021/acs.jctc.8b00880. Epub 2019 Feb 20.

PMID:
30721623
9.

Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field.

Du S, Fu H, Shao X, Chipot C, Cai W.

J Chem Theory Comput. 2019 Mar 12;15(3):1841-1847. doi: 10.1021/acs.jctc.8b00972. Epub 2019 Feb 7.

PMID:
30677293
10.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749. doi: 10.1021/acs.jctc.8b01075. Epub 2018 Nov 27. No abstract available.

PMID:
30480445
11.

Conformational transitions of the serotonin 5-HT3 receptor.

Polovinkin L, Hassaine G, Perot J, Neumann E, Jensen AA, Lefebvre SN, Corringer PJ, Neyton J, Chipot C, Dehez F, Schoehn G, Nury H.

Nature. 2018 Nov;563(7730):275-279. doi: 10.1038/s41586-018-0672-3. Epub 2018 Oct 31.

12.

Re-evaluating the p7 viroporin structure.

Oestringer BP, Bolivar JH, Hensen M, Claridge JK, Chipot C, Dehez F, Holzmann N, Zitzmann N, Schnell JR.

Nature. 2018 Oct;562(7727):E8-E18. doi: 10.1038/s41586-018-0561-9. Epub 2018 Oct 17. No abstract available.

PMID:
30333582
13.

Dynamics and interactions of AAC3 in DPC are not functionally relevant.

Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P.

Nat Struct Mol Biol. 2018 Sep;25(9):745-747. doi: 10.1038/s41594-018-0127-4. No abstract available.

14.

Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions.

Zhang H, Fu H, Shao X, Chipot C, Monari A, Dehez F, Cai W.

Phys Chem Chem Phys. 2018 Sep 12;20(35):22645-22651. doi: 10.1039/c8cp03836h.

PMID:
30132482
15.

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys.

Fu H, Zhang H, Chen H, Shao X, Chipot C, Cai W.

J Phys Chem Lett. 2018 Aug 16;9(16):4738-4745. doi: 10.1021/acs.jpclett.8b01994. Epub 2018 Aug 7.

PMID:
30074802
16.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

Chen H, Fu H, Shao X, Chipot C, Cai W.

J Chem Inf Model. 2018 Jul 23;58(7):1315-1318. doi: 10.1021/acs.jcim.8b00115. Epub 2018 Jun 18.

PMID:
29874076
17.

Link between Membrane Composition and Permeability to Drugs.

Tse CH, Comer J, Wang Y, Chipot C.

J Chem Theory Comput. 2018 Jun 12;14(6):2895-2909. doi: 10.1021/acs.jctc.8b00272. Epub 2018 May 30.

PMID:
29771515
18.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.

Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P.

Chem Rev. 2018 Apr 11;118(7):3559-3607. doi: 10.1021/acs.chemrev.7b00570. Epub 2018 Feb 28. Review.

19.

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

Fu H, Gumbart JC, Chen H, Shao X, Cai W, Chipot C.

J Chem Inf Model. 2018 Mar 26;58(3):556-560. doi: 10.1021/acs.jcim.7b00695. Epub 2018 Feb 16.

20.

How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.

Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P.

J Phys Chem Lett. 2018 Mar 1;9(5):933-938. doi: 10.1021/acs.jpclett.8b00269. Epub 2018 Feb 8.

21.

α-Helix Unwinding as Force Buffer in Spectrins.

Takahashi H, Rico F, Chipot C, Scheuring S.

ACS Nano. 2018 Mar 27;12(3):2719-2727. doi: 10.1021/acsnano.7b08973. Epub 2018 Feb 6.

PMID:
29390177
22.

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA.

Zhang H, Gattuso H, Dumont E, Cai W, Monari A, Chipot C, Dehez F.

Molecules. 2018 Jan 25;23(2). pii: E228. doi: 10.3390/molecules23020228.

23.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

Suh D, Radak BK, Chipot C, Roux B.

J Chem Phys. 2018 Jan 7;148(1):014101. doi: 10.1063/1.5004154.

PMID:
29306299
24.

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944. doi: 10.1021/acs.jctc.7b00875. Epub 2017 Nov 22. Erratum in: J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749.

25.

Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity.

Dehez F, Schanda P, King MS, Kunji ERS, Chipot C.

Biophys J. 2017 Dec 5;113(11):2311-2315. doi: 10.1016/j.bpj.2017.09.019. Epub 2017 Oct 20.

26.

The lubricating role of water in the shuttling of rotaxanes.

Fu H, Shao X, Chipot C, Cai W.

Chem Sci. 2017 Jul 1;8(7):5087-5094. doi: 10.1039/c7sc01593c. Epub 2017 May 16.

27.

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies.

Fu H, Cai W, Hénin J, Roux B, Chipot C.

J Chem Theory Comput. 2017 Nov 14;13(11):5173-5178. doi: 10.1021/acs.jctc.7b00791. Epub 2017 Oct 9.

PMID:
28965398
28.

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

Comer J, Schulten K, Chipot C.

J Chem Theory Comput. 2017 Jun 13;13(6):2523-2532. doi: 10.1021/acs.jctc.7b00264. Epub 2017 May 12.

PMID:
28475319
29.

Tribute to Klaus Schulten.

Tajkhorshid E, Chipot C.

J Phys Chem B. 2017 Apr 20;121(15):3203-3205. doi: 10.1021/acs.jpcb.7b02140. No abstract available.

PMID:
28423902
30.

Methodology for the Simulation of Molecular Motors at Different Scales.

Singharoy A, Chipot C.

J Phys Chem B. 2017 Apr 20;121(15):3502-3514. doi: 10.1021/acs.jpcb.6b09350. Epub 2016 Nov 30.

31.

Structural and energetic study of cation-π-cation interactions in proteins.

Pinheiro S, Soteras I, Gelpí JL, Dehez F, Chipot C, Luque FJ, Curutchet C.

Phys Chem Chem Phys. 2017 Apr 12;19(15):9849-9861. doi: 10.1039/c6cp08448f.

32.

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations.

Zhao T, Fu H, Lelièvre T, Shao X, Chipot C, Cai W.

J Chem Theory Comput. 2017 Apr 11;13(4):1566-1576. doi: 10.1021/acs.jctc.7b00032. Epub 2017 Mar 15.

PMID:
28253446
33.

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

Singharoy A, Chipot C, Moradi M, Schulten K.

J Am Chem Soc. 2017 Jan 11;139(1):293-310. doi: 10.1021/jacs.6b10744. Epub 2016 Dec 23.

34.

Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations.

Gattuso H, Dumont E, Chipot C, Monari A, Dehez F.

Phys Chem Chem Phys. 2016 Dec 7;18(48):33180-33186.

PMID:
27892573
35.

Subdiffusion in Membrane Permeation of Small Molecules.

Chipot C, Comer J.

Sci Rep. 2016 Nov 2;6:35913. doi: 10.1038/srep35913.

36.

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

Gattuso H, Durand E, Bignon E, Morell C, Georgakilas AG, Dumont E, Chipot C, Dehez F, Monari A.

J Phys Chem Lett. 2016 Oct 6;7(19):3760-3765. Epub 2016 Sep 13.

PMID:
27612215
37.

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters.

Bozzi AT, Bane LB, Weihofen WA, McCabe AL, Singharoy A, Chipot CJ, Schulten K, Gaudet R.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10310-5. doi: 10.1073/pnas.1607734113. Epub 2016 Aug 29.

38.

Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments.

Holzmann N, Chipot C, Penin F, Dehez F.

Bioorg Med Chem. 2016 Oct 15;24(20):4920-4927. doi: 10.1016/j.bmc.2016.07.063. Epub 2016 Jul 29.

PMID:
27501910
39.

Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.

Jo S, Suh D, He Z, Chipot C, Roux B.

J Phys Chem B. 2016 Aug 25;120(33):8733-42. doi: 10.1021/acs.jpcb.6b05125. Epub 2016 Aug 3.

PMID:
27409349
40.

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations.

Fu H, Shao X, Chipot C, Cai W.

J Chem Theory Comput. 2016 Aug 9;12(8):3506-13. doi: 10.1021/acs.jctc.6b00447. Epub 2016 Jul 20.

PMID:
27398726
41.

High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale.

Miyagi A, Chipot C, Rangl M, Scheuring S.

Nat Nanotechnol. 2016 Sep;11(9):783-90. doi: 10.1038/nnano.2016.89. Epub 2016 Jun 6.

PMID:
27271964
42.

AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

Ramadoss V, Dehez F, Chipot C.

J Chem Inf Model. 2016 Jun 27;56(6):1122-6. doi: 10.1021/acs.jcim.6b00162. Epub 2016 May 31.

PMID:
27214306
43.

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC.

J Chem Inf Model. 2016 Apr 25;56(4):721-33. doi: 10.1021/acs.jcim.6b00022. Epub 2016 Apr 14.

44.

Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.

Vuković L, Chipot C, Makino DL, Conti E, Schulten K.

J Am Chem Soc. 2016 Mar 30;138(12):4069-78. doi: 10.1021/jacs.5b12065. Epub 2016 Mar 21.

45.

Decrypting protein insertion through the translocon with free-energy calculations.

Gumbart JC, Chipot C.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1663-71. doi: 10.1016/j.bbamem.2016.02.017. Epub 2016 Feb 16. Review.

46.

The true nature of rotary movements in rotaxanes.

Liu P, Shao X, Chipot C, Cai W.

Chem Sci. 2016 Jan 1;7(1):457-462. doi: 10.1039/c5sc03022f. Epub 2015 Oct 13.

47.

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.

Comer J, Phillips JC, Schulten K, Chipot C.

J Chem Theory Comput. 2014 Dec 9;10(12):5276-85. doi: 10.1021/ct500874p. Epub 2014 Nov 26.

PMID:
26583211
48.

Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.

Jo S, Chipot C, Roux B.

J Chem Theory Comput. 2015 May 12;11(5):2234-44. doi: 10.1021/ct501034w. Epub 2015 Apr 21.

PMID:
26574422
49.

Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes.

Fu H, Comer J, Cai W, Chipot C.

J Phys Chem Lett. 2015 Feb 5;6(3):413-8. doi: 10.1021/jz502513w. Epub 2015 Jan 16.

PMID:
26261957
50.

Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution.

Liu P, Shao X, Chipot C, Cai W.

Phys Chem Chem Phys. 2014 Nov 28;16(44):24169-72. doi: 10.1039/c4cp04200j.

PMID:
25311103

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