ArticleBMC structural biology2008
Fast dynamics perturbation analysis for prediction of protein functional sites.
Article in BMC structural biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Coxsackievirus A6 was the predominant pathogen of hand, foot, and mouth disease with frequent recombination and mutations in Shandong Province, 2023.Virus evolution · 2026Article
- Quantitative Characterization of the Impact of Protein-Protein Interactions on Ligand-Protein Binding: A Multi-Chain Dynamics Perturbation Analysis Method.International journal of molecular sciences · 2024Article
- Antimicrobial and anti-biofilm activity of a thiazolidinone derivative againstMicrobiology spectrum · 2024Article
- A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions.BMC bioinformatics · 2022Article
- Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.BMC bioinformatics · 2018Article
- Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes.Biophysics and physicobiology · 2016Article
- Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD-BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate.International journal of molecular sciences · 2015Article
- Literature mining of protein-residue associations with graph rules learned through distant supervision.Journal of biomedical semantics · 2012Article
- Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.Journal of chemical theory and computation · 2012Article
- Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.Journal of the Royal Society, Interface · 2012Review
- Text mining improves prediction of protein functional sites.PloS one · 2012Article
- Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.Protein science : a publication of the Protein Society · 2011Article
- Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.Protein science : a publication of the Protein Society · 2010Article
- Elastic network model of allosteric regulation in protein kinase PDK1.BMC structural biology · 2010Article
- Protein pockets: inventory, shape, and comparison.Journal of chemical information and modeling · 2010Article
- Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.Journal of chemical theory and computation · 2009Article
- Coarse-grained modeling of allosteric regulation in protein receptors.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model.BMC structural biology · 2009Article
- Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.PLoS computational biology · 2009Article
- Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe present a fast version of the dynamics perturbation analysis (DPA) algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites.
resultsThe Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues) were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues) were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm.
conclusionCompared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.
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.