ArticlePloS one2015
Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 257 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
257 citing papers in PubMed.
- Article
- Mechanistic Insights into Poloxamer 188-Mediated Stabilization of AAV8 Capsids Using Coarse-Grained Molecular Dynamics.Pharmaceutical research · 2026Article
- Lipase ITB 2.1: a structure- and function-validated model for anti-obesity drug screening.Molecular diversity · 2026Article
- Bioactive compounds from marine algae targeting MMP-9: A computational approach to rheumatoid arthritis treatment.Medicine · 2026Article
- Molecular insights and ADMET profiling of iridoids as candidate leads for erectile dysfunction therapy.Journal of molecular modeling · 2026Article
- Kinetic Compatibility as a Predictor of PTP1B Inhibitor Combination Outcomes: An Integrated Experimental and Computational Study.ChemMedChem · 2026Article
- Natural chlocarbazomycins as potential adenosine A1 receptor antagonists: ligand-based and structure-based virtual screening, quantum chemical analysis and CNS MPO study.Molecular diversity · 2026Article
- An integrated computational strategy for profiling terpenoid for dual-target leads against Klebsiella pneumoniae penicillin-binding protein 3 and beta-lactamase.Molecular diversity · 2026Article
- DFT design of PORSC advances · 2026Article
- Explainable Artificial Intelligence (XAI) and Molecular Modeling Techniques to Discover Putative HER2 Inhibitors.International journal of molecular sciences · 2026Article
- Potential for the Terminal SKP1 Glycosyltransferase to Exert Non-Enzymatic Control of SKP1 inbioRxiv : the preprint server for biology · 2026Article
- Comparative genomic analysis of RNA-binding proteins across some drug resistant and sensitive Staphylococcus aureus.Applied microbiology and biotechnology · 2026Article
- Designing potent and immunogenic epitope based peptide vaccine against all serotypes of DENV via structural, physico-chemical and immunoinformatics-based approaches.Scientific reports · 2026Article
- Comprehensive metabolomic profiling of Egyptian Salvia species reveals promising leads for chemopreventive and anti-inflammatory drug development: In vitro and In silico study.Scientific reports · 2026Article
- GC-MS-Based Metabolomic Insights Into Fermentation-Induced Bioactive Compounds and Metabolic Health-Related Activities of White Corn Steep Liquor.Food science & nutrition · 2026Article
- Protonation of Key Acidic Residues Reveals Binding Features of PCABs to Gastric H, K-ATPase.The Journal of membrane biology · 2026Article
- The "Survivor Peptide" Hypothesis: Structural Resilience and Immunological Persistence of Food Allergens in the Gut-Mammary Axis.Nutrients · 2026Review
- Isolation, Bromination, and Antimicrobial Activity of 3-Ethyl-4-hydroxy-6-methyl-Antibiotics (Basel, Switzerland) · 2026Article
- Rational design framework for fluorescent biosensors from periplasmic binding proteins.Bioscience reports · 2026Article
- Utilizing drugs, food, and natural product libraries: A computational approach to targeting PGAM1 in clinical cancer therapy.Medicine · 2026Article
197 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.