ArticleJournal of computational chemistry2014
Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
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- ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis.bioRxiv : the preprint server for biology · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A.Nature communications · 2025Article
- Mechanism of phosphoinositide regulation of lysosomal pH via inhibition of CLC-7.bioRxiv : the preprint server for biology · 2025Article
- Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.Cell reports. Physical science · 2025Article
- Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.Journal of chemical information and modeling · 2025Article
- Effects of Nicotine on the Thermodynamics and Phase Coexistence of Pulmonary Surfactant Model Membranes.Membranes · 2024Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Long-Time Scale Simulations Reveal Key Dynamics That Drive the Onset of the N State in the Proteorhodopsin Photocycle.The journal of physical chemistry. B · 2024Article
- System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.The Journal of chemical physics · 2024Article
- Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations.Biochimica et biophysica acta. Biomembranes · 2024Article
- Machine-learned molecular mechanics force fields from large-scale quantum chemical data.Chemical science · 2024Article
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Structural basis for partial agonism in 5-HTNature structural & molecular biology · 2024Article
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.PloS one · 2024Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.
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Registered trials
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