These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

165 related articles for article (PubMed ID: 36378163)

  • 1. PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method.
    Chen CG; Nardi AN; Amadei A; D'Abramo M
    J Chem Theory Comput; 2023 Jan; 19(1):33-41. PubMed ID: 36378163
    [TBL] [Abstract][Full Text] [Related]  

  • 2. INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations.
    Cofer-Shabica DV; Menger MFSJ; Ou Q; Shao Y; Subotnik JE; Faraji S
    J Chem Theory Comput; 2022 Aug; 18(8):4601-4614. PubMed ID: 35901266
    [TBL] [Abstract][Full Text] [Related]  

  • 3. MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.
    Cárdenas G; Lucia-Tamudo J; Mateo-delaFuente H; Palmisano VF; Anguita-Ortiz N; Ruano L; Pérez-Barcia Á; Díaz-Tendero S; Mandado M; Nogueira JJ
    J Comput Chem; 2023 Feb; 44(4):516-533. PubMed ID: 36507763
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H; Lu Z; Parks JM; Burger SK; Yang W
    J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486
    [TBL] [Abstract][Full Text] [Related]  

  • 5. MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.
    Raghavan B; Schackert FK; Levy A; Johnson SK; Ippoliti E; Mandelli D; Olsen JMH; Rothlisberger U; Carloni P
    J Chem Inf Model; 2023 Mar; 63(5):1406-1412. PubMed ID: 36811959
    [TBL] [Abstract][Full Text] [Related]  

  • 6. An extensible interface for QM/MM molecular dynamics simulations with AMBER.
    Götz AW; Clark MA; Walker RC
    J Comput Chem; 2014 Jan; 35(2):95-108. PubMed ID: 24122798
    [TBL] [Abstract][Full Text] [Related]  

  • 7. The roles of electronic exchange and correlation in charge-transfer- to-solvent dynamics: Many-electron nonadiabatic mixed quantum/classical simulations of photoexcited sodium anions in the condensed phase.
    Glover WJ; Larsen RE; Schwartz BJ
    J Chem Phys; 2008 Oct; 129(16):164505. PubMed ID: 19045282
    [TBL] [Abstract][Full Text] [Related]  

  • 8. COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.
    Weingart O; Nenov A; Altoè P; Rivalta I; Segarra-Martí J; Dokukina I; Garavelli M
    J Mol Model; 2018 Sep; 24(9):271. PubMed ID: 30178229
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.
    de la Lande A; Alvarez-Ibarra A; Hasnaoui K; Cailliez F; Wu X; Mineva T; Cuny J; Calaminici P; López-Sosa L; Geudtner G; Navizet I; Garcia Iriepa C; Salahub DR; Köster AM
    Molecules; 2019 Apr; 24(9):. PubMed ID: 31035516
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.
    Riahi S; Rowley CN
    J Comput Chem; 2014 Oct; 35(28):2076-86. PubMed ID: 25178266
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States.
    De Vetta M; Baig O; Steen D; Nogueira JJ; González L
    Molecules; 2018 Nov; 23(11):. PubMed ID: 30424014
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics.
    Mehmood R; Kulik HJ
    Methods Mol Biol; 2022; 2397():227-248. PubMed ID: 34813067
    [TBL] [Abstract][Full Text] [Related]  

  • 13. QM/MM-MD simulations of conjugated polyelectrolytes: a study of luminescent conjugated oligothiophenes for use as biophysical probes.
    Sjöqvist J; Linares M; Mikkelsen KV; Norman P
    J Phys Chem A; 2014 May; 118(19):3419-28. PubMed ID: 24738472
    [TBL] [Abstract][Full Text] [Related]  

  • 14. QM/MM modeling of environmental effects on electronic transitions of the FMO complex.
    Gao J; Shi WJ; Ye J; Wang X; Hirao H; Zhao Y
    J Phys Chem B; 2013 Apr; 117(13):3488-95. PubMed ID: 23480507
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Solvent Effects on Electronically Excited States: QM/Continuum Versus QM/Explicit Models.
    De Vetta M; Menger MFSJ; Nogueira JJ; González L
    J Phys Chem B; 2018 Mar; 122(11):2975-2984. PubMed ID: 29481750
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM.
    Avagliano D; Bonfanti M; Nenov A; Garavelli M
    J Comput Chem; 2022 Sep; 43(24):1641-1655. PubMed ID: 35815854
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs.
    Shen C; Wang X; He X
    Front Chem; 2021; 9():801062. PubMed ID: 35004616
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.
    Koch DM; Peslherbe GH
    J Phys Chem B; 2008 Jan; 112(2):636-49. PubMed ID: 18183959
    [TBL] [Abstract][Full Text] [Related]  

  • 19. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics.
    Pederson JP; McDaniel JG
    J Chem Phys; 2024 Jul; 161(3):. PubMed ID: 39007371
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.
    Ould Mohamed L; Abtouche S; Ghoualem Z; Assfeld X
    J Mol Model; 2024 May; 30(6):180. PubMed ID: 38780881
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.