ArticleJournal of chemical theory and computation2006
A New Method for Coarse-Grained Elastic Normal-Mode Analysis.
Article in Journal of chemical theory and computation, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
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- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.PLoS computational biology · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.The Journal of chemical physics · 2021Article
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- Article
- Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates.PloS one · 2021Article
- Predicting Protein Functional Motions: an Old Recipe with a New Twist.Biophysical journal · 2020Article
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling.Proteins · 2017Article
- DynOmics: dynamics of structural proteome and beyond.Nucleic acids research · 2017Article
- Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling.Biophysical journal · 2017Article
- Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data.Structural dynamics (Melville, N.Y.) · 2017Article
- Atomic description of the immune complex involved in heparin-induced thrombocytopenia.Nature communications · 2015Article
- Elastic network models capture the motions apparent within ensembles of RNA structures.RNA (New York, N.Y.) · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- FlexE: Using elastic network models to compare models of protein structure.Journal of chemical theory and computation · 2012Article
- fSUB: normal mode analysis with flexible substructures.The journal of physical chemistry. B · 2012Article
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Authors and funding
3 authors.
Funding
Abstract
In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The purpose is to overcome a long-standing problem in the conventional analysis called the tip effect that makes the motional patterns (eigenvectors) of some low-frequency modes irrational. The new method retains the merits of a conventional method such as not requiring lengthy initial energy minimization, which always distorts structures, and also delivers substantially more accurate low-frequency modes with no tip effect for proteins of any size. This improvement of modes is crucial for certain types of applications such as structural refinement or normal-mode-based sampling.
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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.