BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

404 related articles for article (PubMed ID: 37431910)

  • 21. Recent advances toward a general purpose linear-scaling quantum force field.
    Giese TJ; Huang M; Chen H; York DM
    Acc Chem Res; 2014 Sep; 47(9):2812-20. PubMed ID: 24937206
    [TBL] [Abstract][Full Text] [Related]  

  • 22. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.
    Suh D; Arattu Thodika AR; Kim S; Nam K; Im W
    J Chem Theory Comput; 2024 Jun; 20(12):5337-5351. PubMed ID: 38856971
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations.
    Gallardo A; Bogart BM; Dutagaci B
    J Chem Inf Model; 2022 Jun; 62(12):3079-3089. PubMed ID: 35686985
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.
    Lin FY; Huang J; Pandey P; Rupakheti C; Li J; Roux BT; MacKerell AD
    J Chem Theory Comput; 2020 May; 16(5):3221-3239. PubMed ID: 32282198
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments.
    Lahey SJ; Thien Phuc TN; Rowley CN
    J Chem Inf Model; 2020 Dec; 60(12):6258-6268. PubMed ID: 33263401
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Large-Scale Atomic Simulation via Machine Learning Potentials Constructed by Global Potential Energy Surface Exploration.
    Kang PL; Shang C; Liu ZP
    Acc Chem Res; 2020 Oct; 53(10):2119-2129. PubMed ID: 32940999
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G; Pastore A; Piazza F; Temussi PA
    Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Systematic Differences between Current Molecular Dynamics Force Fields To Represent Local Properties of Intrinsically Disordered Proteins.
    Yu L; Li DW; Brüschweiler R
    J Phys Chem B; 2021 Jan; 125(3):798-804. PubMed ID: 33444020
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Assessing the Current State of Amber Force Field Modifications for DNA.
    Galindo-Murillo R; Robertson JC; Zgarbová M; Šponer J; Otyepka M; Jurečka P; Cheatham TE
    J Chem Theory Comput; 2016 Aug; 12(8):4114-27. PubMed ID: 27300587
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Accurate non-bonded potentials based on periodic quantum mechanics calculations for use in molecular simulations of materials and systems.
    Naserifar S; Oppenheim JJ; Yang H; Zhou T; Zybin S; Rizk M; Goddard WA
    J Chem Phys; 2019 Oct; 151(15):154111. PubMed ID: 31640352
    [TBL] [Abstract][Full Text] [Related]  

  • 31. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
    Vanommeslaeghe K; Hatcher E; Acharya C; Kundu S; Zhong S; Shim J; Darian E; Guvench O; Lopes P; Vorobyov I; Mackerell AD
    J Comput Chem; 2010 Mar; 31(4):671-90. PubMed ID: 19575467
    [TBL] [Abstract][Full Text] [Related]  

  • 32. BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations.
    Lier B; Poliak P; Marquetand P; Westermayr J; Oostenbrink C
    J Phys Chem Lett; 2022 May; 13(17):3812-3818. PubMed ID: 35467875
    [TBL] [Abstract][Full Text] [Related]  

  • 33. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
    Lee J; Cheng X; Swails JM; Yeom MS; Eastman PK; Lemkul JA; Wei S; Buckner J; Jeong JC; Qi Y; Jo S; Pande VS; Case DA; Brooks CL; MacKerell AD; Klauda JB; Im W
    J Chem Theory Comput; 2016 Jan; 12(1):405-13. PubMed ID: 26631602
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
    Aliev AE; Courtier-Murias D
    J Phys Chem B; 2010 Sep; 114(38):12358-75. PubMed ID: 20825228
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Fragment quantum mechanical calculation of proteins and its applications.
    He X; Zhu T; Wang X; Liu J; Zhang JZ
    Acc Chem Res; 2014 Sep; 47(9):2748-57. PubMed ID: 24851673
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.
    Lev B; Roux B; Noskov SY
    J Chem Theory Comput; 2013 Sep; 9(9):4165-75. PubMed ID: 26592407
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Some practical approaches to treating electrostatic polarization of proteins.
    Ji C; Mei Y
    Acc Chem Res; 2014 Sep; 47(9):2795-803. PubMed ID: 24883956
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.
    Rupakheti CR; MacKerell AD; Roux B
    J Chem Theory Comput; 2021 Nov; 17(11):7085-7095. PubMed ID: 34609863
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior.
    Biswas PK; Vellore NA; Yancey JA; Kucukkal TG; Collier G; Brooks BR; Stuart SJ; Latour RA
    J Comput Chem; 2012 Jun; 33(16):1458-66. PubMed ID: 22488548
    [TBL] [Abstract][Full Text] [Related]  

  • 40. The QM-MM interface for CHARMM-deMon.
    Lev B; Zhang R; de la Lande A; Salahub D; Noskov SY
    J Comput Chem; 2010 Apr; 31(5):1015-23. PubMed ID: 20027641
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 21.