ReviewEMBO reports2008
Molecular simulations of protein dynamics: new windows on mechanisms in biology.
Review in EMBO reports, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed.
- Positive correlation between structural disorder of the HIV-1 Gag N-terminal segment and progeny virus particle formation.Journal of virology · 2025Article
- Activating mutations drive human MEK1 kinase using a gear-shifting mechanism.The Biochemical journal · 2023Article
- Modeling the Homologous Recombination Process: Methods, Successes and Challenges.International journal of molecular sciences · 2023Review
- Article
- YfeX - A New Platform for Carbene Transferase Development with High Intrinsic Reactivity.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study.Physical chemistry chemical physics : PCCP · 2021Article
- Article
- Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1.Scientific reports · 2021Article
- Allosteric Regulation of HIV-1 Capsid Structure for Gag Assembly, Virion Production, and Viral Infectivity by a Disordered Interdomain Linker.Journal of virology · 2019Article
- Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses.Progress in biophysics and molecular biology · 2019Review
- Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism inBiomolecules · 2019Article
- Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications.International journal of molecular sciences · 2019Review
- How peptide/MHC presence affects the dynamics of the LC13 T-cell receptor.Scientific reports · 2019Article
- Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders.Computational and structural biotechnology journal · 2019Article
- Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.The journal of physical chemistry. B · 2018Article
- Conformational Stability of the Hemagglutinin of H5N1 Influenza A Viruses Influences Susceptibility to Broadly Neutralizing Stem Antibodies.Journal of virology · 2018Article
- Taxifolin as dual inhibitor of Mtb DNA gyrase and isoleucyl-tRNA synthetase: in silico molecular docking, dynamics simulation and in vitro assays.In silico pharmacology · 2018Article
- Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods.Journal of computer-aided molecular design · 2017Article
- A new class of enhanced kinetic sampling methods for building Markov state models.The Journal of chemical physics · 2017Article
- ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability.Nature communications · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Recent advances in computer hardware and software have led to the development of increasingly successful molecular simulations of protein structural dynamics that are intrinsic to biological processes. These simulations have resulted in models that increasingly agree with experimental observations, suggest new experiments and provide insights into biological mechanisms. Used in combination with data obtained with sophisticated experimental techniques, simulations are helping us to understand biological complexity at the atomic and molecular levels and are giving promising insights into the genetic, thermodynamic and functional/mechanistic behaviour of biological processes. Here, we highlight some examples of such approaches that illustrate the current state and potential of the field of molecular simulation.
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.