ArticleThe Journal of chemical physics2008
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.
Article in The Journal of chemical physics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis.Journal of chemical theory and computation · 2024Article
- Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.International journal of molecular sciences · 2023Article
- Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.Acta crystallographica. Section D, Structural biology · 2023Article
- Surveying nonvisual arrestins reveals allosteric interactions between functional sites.Proteins · 2023Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin.Journal of chemical theory and computation · 2021Article
- Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations.Scientific reports · 2021Article
- Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.The Journal of chemical physics · 2021Article
- A revised formulation of the generalized subsystem vibrational analysis (GSVA).Theoretical chemistry accounts · 2021Article
- Multi-level free energy simulation with a staged transformation approach.The Journal of chemical physics · 2020Article
- Frequency Range Selection Method for Vibrational Spectra.The journal of physical chemistry letters · 2018Article
- Dissecting conformational changes in APP's transmembrane domain linked to ε-efficiency in familial Alzheimer's disease.PloS one · 2018Article
- Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.PLoS computational biology · 2015Article
- Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.Biochimica et biophysica acta · 2015Article
- Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.The journal of physical chemistry. A · 2015Article
- Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.Journal of computational chemistry · 2014Article
- Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.Journal of chemical theory and computation · 2014Article
- The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.Proteins · 2013Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Elastic Network Models are Robust to Variations in Formalism.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the "tip effect" in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
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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.