ArticleFrontiers in molecular biosciences2015
Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.
Article in Frontiers in molecular biosciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed.
- Selection of Novel DNA Aptamers against HPV16 Biomarker, E6: AnACS omega · 2026Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Unraveling membrane properties at the organelle-level with LipidDyn.Computational and structural biotechnology journal · 2022Article
- Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Modeling of the thermal properties of SARS-CoV-2 S-protein.Frontiers in molecular biosciences · 2022Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer.Journal of enzyme inhibition and medicinal chemistry · 2020Article
- Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations.Scientific reports · 2020Article
- A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy.Scientific reports · 2020Article
- Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy.Journal of computer-aided molecular design · 2020Article
- Review
- Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques.Frontiers in cell and developmental biology · 2020Review
- Understanding the structural details of APOBEC3-DNA interactions using graph-based representations.Current research in structural biology · 2020Article
- Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case.Frontiers in molecular biosciences · 2020Review
- A Time-Dependent Quantum Approach to Allostery and a Comparison With Light-Harvesting in Photosynthetic Phenomenon.Frontiers in molecular biosciences · 2020Article
- Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level.PLoS computational biology · 2019Article
- Effects of Membrane and Biological Target on the Structural and Allosteric Properties of Recoverin: A Computational Approach.International journal of molecular sciences · 2019Article
- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.Nucleic acids research · 2019Article
- Evolutionary-Conserved Allosteric Properties of Three Neuronal Calcium Sensor Proteins.Frontiers in molecular neuroscience · 2019Article
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
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
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.