119 related articles for article (PubMed ID: 33512157)
1. Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations.
Ries B; Linker SM; Hahn DF; König G; Riniker S
J Chem Inf Model; 2021 Feb; 61(2):560-564. PubMed ID: 33512157
[TBL] [Abstract][Full Text] [Related]
2. Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
Parton DL; Grinaway PB; Hanson SM; Beauchamp KA; Chodera JD
PLoS Comput Biol; 2016 Jun; 12(6):e1004728. PubMed ID: 27337644
[TBL] [Abstract][Full Text] [Related]
3. MD DaVis: interactive data visualization of protein molecular dynamics.
Maity D; Pal D
Bioinformatics; 2022 Jun; 38(12):3299-3301. PubMed ID: 35532115
[TBL] [Abstract][Full Text] [Related]
4. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.
Pool R; Heringa J; Hoefling M; Schulz R; Smith JC; Feenstra KA
J Comput Chem; 2012 May; 33(12):1207-14. PubMed ID: 22370965
[TBL] [Abstract][Full Text] [Related]
5. FATSLiM: a fast and robust software to analyze MD simulations of membranes.
Buchoux S
Bioinformatics; 2017 Jan; 33(1):133-134. PubMed ID: 27578804
[TBL] [Abstract][Full Text] [Related]
6. WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.
Yang DT; Chong LT
bioRxiv; 2024 May; ():. PubMed ID: 38826259
[TBL] [Abstract][Full Text] [Related]
7. NGLview-interactive molecular graphics for Jupyter notebooks.
Nguyen H; Case DA; Rose AS
Bioinformatics; 2018 Apr; 34(7):1241-1242. PubMed ID: 29236954
[TBL] [Abstract][Full Text] [Related]
8. Testing for physical validity in molecular simulations.
Merz PT; Shirts MR
PLoS One; 2018; 13(9):e0202764. PubMed ID: 30188933
[TBL] [Abstract][Full Text] [Related]
9. NeuroPycon: An open-source python toolbox for fast multi-modal and reproducible brain connectivity pipelines.
Meunier D; Pascarella A; Altukhov D; Jas M; Combrisson E; Lajnef T; Bertrand-Dubois D; Hadid V; Alamian G; Alves J; Barlaam F; Saive AL; Dehgan A; Jerbi K
Neuroimage; 2020 Oct; 219():117020. PubMed ID: 32522662
[TBL] [Abstract][Full Text] [Related]
10. MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics.
de Sancho D; Aguirre A
J Chem Inf Model; 2019 Sep; 59(9):3625-3629. PubMed ID: 31423789
[TBL] [Abstract][Full Text] [Related]
11. gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.
Irrgang ME; Hays JM; Kasson PM
Bioinformatics; 2018 Nov; 34(22):3945-3947. PubMed ID: 29912282
[TBL] [Abstract][Full Text] [Related]
12. MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations.
Liu H; Jin Y; Ding H
Brief Bioinform; 2023 Mar; 24(2):. PubMed ID: 36790845
[TBL] [Abstract][Full Text] [Related]
13. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS.
Vieira IHP; Botelho EB; de Souza Gomes TJ; Kist R; Caceres RA; Zanchi FB
BMC Bioinformatics; 2023 Mar; 24(1):107. PubMed ID: 36949402
[TBL] [Abstract][Full Text] [Related]
14. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
Michaud-Agrawal N; Denning EJ; Woolf TB; Beckstein O
J Comput Chem; 2011 Jul; 32(10):2319-27. PubMed ID: 21500218
[TBL] [Abstract][Full Text] [Related]
15. pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules.
Ramos MC; Quoika PK; Horta VAC; Dias DM; Costa EG; do Amaral JLM; Ribeiro LM; Liedl KR; Horta BAC
J Chem Inf Model; 2021 Apr; 61(4):1539-1544. PubMed ID: 33819017
[TBL] [Abstract][Full Text] [Related]
16. ProtPOS: a python package for the prediction of protein preferred orientation on a surface.
Ngai JC; Mak PI; Siu SW
Bioinformatics; 2016 Aug; 32(16):2537-8. PubMed ID: 27153619
[TBL] [Abstract][Full Text] [Related]
17. MD-TASK: a software suite for analyzing molecular dynamics trajectories.
Brown DK; Penkler DL; Sheik Amamuddy O; Ross C; Atilgan AR; Atilgan C; Tastan Bishop Ö
Bioinformatics; 2017 Sep; 33(17):2768-2771. PubMed ID: 28575169
[TBL] [Abstract][Full Text] [Related]
18. Gro2mat: a package to efficiently read gromacs output in MATLAB.
Dien H; Deane CM; Knapp B
J Comput Chem; 2014 Jul; 35(20):1528-31. PubMed ID: 24920464
[TBL] [Abstract][Full Text] [Related]
19. CaFE: a tool for binding affinity prediction using end-point free energy methods.
Liu H; Hou T
Bioinformatics; 2016 Jul; 32(14):2216-8. PubMed ID: 27153651
[TBL] [Abstract][Full Text] [Related]
20. myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.
Kasahara K; Terazawa H; Itaya H; Goto S; Nakamura H; Takahashi T; Higo J
Biophys Physicobiol; 2020; 17():140-146. PubMed ID: 33240741
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]