ArticleHeliyon2016
Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.
Article in Heliyon, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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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.
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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.
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Who cites it
8 citing papers in PubMed.
- OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information.Molecules (Basel, Switzerland) · 2025Article
- Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.Journal of chemical theory and computation · 2024Article
- In silico analysis and molecular docking studies of natural compounds of Withania somnifera against bovine NLRP9.Journal of molecular modeling · 2023Article
- Insights into receptor structure and dynamics at the surface of living cells.Nature communications · 2023Article
- Article
- Sequence-specific dynamic information in proteins.Proteins · 2019Article
- Remote Activation of a Latent Epitope in an Autoantigen Decoded With Simulated B-Factors.Frontiers in immunology · 2019Article
- How large B-factors can be in protein crystal structures.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å
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