Boosting the Full Potential of PyMOL with Structural Biology Plugins
Abstract
:1. Introduction
2. Protein Sequences and Structures Analyses (PSSAs)
2.1. PyMod
2.2. pyProGA
2.3. MPBuilder
2.4. ProBiS H2O, ProBiS H2O MD and Waterdock 2.0
2.5. iPBAvizu
2.6. DCA-MOL
3. Protein-Ligand Interactions
3.1. DockingPie
3.2. DRUGpy
3.3. PoseFilter
4. Protein Dynamics
4.1. Geo-Measures
4.2. Enlighten2
4.3. pyMODE-TASK
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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Name | Description | Release Date |
---|---|---|
DockingPie | A platform for molecular and consensus docking (PLI) | 2022 |
PyMod | Environment for structural bioinformatics (PSSAs) | 2021 |
pyProGA | Analysis of static protein residue networks (PSSAs) | 2021 |
MPBuilder | Building and Refinement of Solubilized Membrane Proteins Against SAXS Data (PSSAs) | 2021 |
PoseFilter | Filtering small molecule conformations ensemble (PLI) | 2021 |
DRUGpy | Druggable hot spots identification (PLI) | 2021 |
Geo-Measures | Analyses of protein structures ensemble (PD) | 2020 |
Enlighten2 | A platform for MD simulations (PD) | 2020 |
ProBiS H2O MD | MD-based prediction of conserved water sites (PSSAs) | 2020 |
iPBAVizu 1 | Protein structure superposition approach (PSSAs) | 2019 |
DCA-MOL 1 | Analysis of Direct Evolutionary Couplings (PSSAs) | 2019 |
pyMODE-TASK 1 | Environment for MD trajectories analyses (PD) | 2018 |
Waterdock 2.0 | Water placement prediction (PSSAs) | 2017 |
ProBiS H2O | Conserved water sites identification (PSSAs) | 2017 |
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Rosignoli, S.; Paiardini, A. Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules 2022, 12, 1764. https://doi.org/10.3390/biom12121764
Rosignoli S, Paiardini A. Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules. 2022; 12(12):1764. https://doi.org/10.3390/biom12121764
Chicago/Turabian StyleRosignoli, Serena, and Alessandro Paiardini. 2022. "Boosting the Full Potential of PyMOL with Structural Biology Plugins" Biomolecules 12, no. 12: 1764. https://doi.org/10.3390/biom12121764
APA StyleRosignoli, S., & Paiardini, A. (2022). Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules, 12(12), 1764. https://doi.org/10.3390/biom12121764