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 *

132 related articles for article (PubMed ID: 34411332)

  • 21. gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.
    Serçinoglu O; Ozbek P
    Nucleic Acids Res; 2018 Jul; 46(W1):W554-W562. PubMed ID: 29800260
    [TBL] [Abstract][Full Text] [Related]  

  • 22. prepareforleap: An automated tool for fast PDB-to-parameter generation.
    Roe DR; Bergonzo C
    J Comput Chem; 2022 May; 43(13):930-935. PubMed ID: 35318701
    [TBL] [Abstract][Full Text] [Related]  

  • 23. CHARMM-GUI 10 years for biomolecular modeling and simulation.
    Jo S; Cheng X; Lee J; Kim S; Park SJ; Patel DS; Beaven AH; Lee KI; Rui H; Park S; Lee HS; Roux B; MacKerell AD; Klauda JB; Qi Y; Im W
    J Comput Chem; 2017 Jun; 38(15):1114-1124. PubMed ID: 27862047
    [TBL] [Abstract][Full Text] [Related]  

  • 24. APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories.
    Lukat G; Krüger J; Sommer B
    J Chem Inf Model; 2013 Nov; 53(11):2908-25. PubMed ID: 24175728
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL.
    Makarewicz T; Kaźmierkiewicz R
    J Chem Inf Model; 2013 May; 53(5):1229-34. PubMed ID: 23611462
    [TBL] [Abstract][Full Text] [Related]  

  • 26. RIP-MD: a tool to study residue interaction networks in protein molecular dynamics.
    Contreras-Riquelme S; Garate JA; Perez-Acle T; Martin AJM
    PeerJ; 2018; 6():e5998. PubMed ID: 30568854
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.
    Kimura SR; Rajamani R; Langley DR
    J Chem Phys; 2011 Dec; 135(23):231101. PubMed ID: 22191857
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.
    Yang L; Skjevik ÅA; Han Du WG; Noodleman L; Walker RC; Götz AW
    Data Brief; 2016 Sep; 8():1209-14. PubMed ID: 27547799
    [TBL] [Abstract][Full Text] [Related]  

  • 29. BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.
    Abrahamsson E; Plotkin SS
    J Mol Graph Model; 2009 Sep; 28(2):140-5. PubMed ID: 19515592
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
    Ditzler MA; Otyepka M; Sponer J; Walter NG
    Acc Chem Res; 2010 Jan; 43(1):40-7. PubMed ID: 19754142
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.
    Khoury GA; Smadbeck J; Tamamis P; Vandris AC; Kieslich CA; Floudas CA
    ACS Synth Biol; 2014 Dec; 3(12):855-69. PubMed ID: 24932669
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Combination of the CHARMM27 force field with united-atom lipid force fields.
    Sapay N; Tieleman DP
    J Comput Chem; 2011 May; 32(7):1400-10. PubMed ID: 21425293
    [TBL] [Abstract][Full Text] [Related]  

  • 33. AceDRG: a stereochemical description generator for ligands.
    Long F; Nicholls RA; Emsley P; Graǽulis S; Merkys A; Vaitkus A; Murshudov GN
    Acta Crystallogr D Struct Biol; 2017 Feb; 73(Pt 2):112-122. PubMed ID: 28177307
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
    Tan C; Jung J; Kobayashi C; Torre DU; Takada S; Sugita Y
    PLoS Comput Biol; 2022 Apr; 18(4):e1009578. PubMed ID: 35381009
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible.
    Zinovjev K; van der Kamp MW
    Bioinformatics; 2020 Dec; 36(20):5104-5106. PubMed ID: 32683443
    [TBL] [Abstract][Full Text] [Related]  

  • 36. MDWiZ: a platform for the automated translation of molecular dynamics simulations.
    Rusu VH; Horta VA; Horta BA; Lins RD; Baron R
    J Mol Graph Model; 2014 Mar; 48():80-6. PubMed ID: 24434017
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model.
    Lemkul JA
    Methods Mol Biol; 2021; 2315():219-240. PubMed ID: 34302679
    [TBL] [Abstract][Full Text] [Related]  

  • 38. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.
    Kim S; Lee J; Jo S; Brooks CL; Lee HS; Im W
    J Comput Chem; 2017 Jun; 38(21):1879-1886. PubMed ID: 28497616
    [TBL] [Abstract][Full Text] [Related]  

  • 39. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.
    Purawat S; Ieong PU; Malmstrom RD; Chan GJ; Yeung AK; Walker RC; Altintas I; Amaro RE
    Biophys J; 2017 Jun; 112(12):2469-2474. PubMed ID: 28636905
    [TBL] [Abstract][Full Text] [Related]  

  • 40. TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.
    Vermaas JV; Hardy DJ; Stone JE; Tajkhorshid E; Kohlmeyer A
    J Chem Inf Model; 2016 Jun; 56(6):1112-6. PubMed ID: 27196035
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 7.