ReviewFrontiers in bioscience : a journal and virtual library2008
Probing protein aggregation using discrete molecular dynamics.
Review in Frontiers in bioscience : a journal and virtual library, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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.
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.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- Parallel in-register contact propensity predicts the Amyloidogenicity of ADan and ABri in familial dementias.International journal of biological macromolecules · 2026Article
- Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions.International journal of molecular sciences · 2025Article
- Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation.Journal of chemical information and modeling · 2024Article
- Exploration of Protein Aggregations in Parkinson's Disease Through Computational Approaches and Big Data Analytics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta.Nano today · 2021Article
- A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2.Journal of chemical information and modeling · 2019Article
- In Silico Methods in Antibody Design.Antibodies (Basel, Switzerland) · 2018Review
- Computational approaches to understanding protein aggregation in neurodegeneration.Journal of molecular cell biology · 2014Review
- On the subject of rigor in the study of amyloid β-protein assembly.Alzheimer's research & therapy · 2013Review
- Computer-aided antibody design.Protein engineering, design & selection : PEDS · 2012Review
- 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
- Article
- Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences.PLoS computational biology · 2010Article
- Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity.Physical chemistry chemical physics : PCCP · 2010Article
- Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the role of biomolecular dynamics in cellular processes leading to human diseases and the ability to rationally manipulate these processes is of fundamental importance in scientific research. The last decade has witnessed significant progress in probing biophysical behavior of proteins. However, we are still limited in understanding how changes in protein dynamics and inter-protein interactions occurring in short length- and time-scales lead to aberrations in their biological function. Bridging this gap in biology probed using computer simulations marks a challenging frontier in computational biology. Here we examine hypothesis-driven simplified protein models in conjunction with discrete molecular dynamics in the study of protein aggregation, implicated in series of neurodegenerative diseases, such as Alzheimer's and Huntington's diseases. Discrete molecular dynamics simulations of simplified protein models have emerged as a powerful methodology with its ability to bridge the gap in time and length scales from protein dynamics to aggregation, and provide an indispensable tool for probing protein aggregation.
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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.