ArticleThe journal of physical chemistry. B2012
Unrestrained computation of free energy along a path.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String.Molecules (Basel, Switzerland) · 2024Article
- Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.Molecules (Basel, Switzerland) · 2024Article
- Experimental and Theoretical Investigation of External Electric-Field-Induced Crystallization of TKX-50 from Solution by Finite-Temperature String with Order Parameters as Collective Variables for Ionic Crystals.Molecules (Basel, Switzerland) · 2024Article
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.Journal of chemical theory and computation · 2022Article
- TYROSINE KINASES: COMPLEX MOLECULAR SYSTEMS CHALLENGING COMPUTATIONAL METHODOLOGIES.The European physical journal. B · 2021Article
- All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.The Journal of chemical physics · 2020Article
- Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization.Journal of chemical theory and computation · 2018Article
- On the accuracy of one- and two-particle solvation entropies.The Journal of chemical physics · 2017Article
- Role of active site conformational changes in photocycle activation of the AppA BLUF photoreceptor.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.Methods in enzymology · 2016Review
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.The Journal of chemical physics · 2014Article
- The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface.MedChemComm · 2013Article
- Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study.Journal of chemical theory and computation · 2013Article
- Efficiently refining a transition path using clustering.Biophysical journal · 2013Article
- Simulating rare events using a weighted ensemble-based string method.The Journal of chemical physics · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We apply the adaptive biasing potential (ABP) method to optimize the principal curve defining a conformational transition between two known end states and to subsequently compute the one-dimensional potential of mean force as a function of arc length along the principal curve. This approach allows the use of the ABP method in a collective variable space of arbitrary dimension and offers several advantages over line-search methods. First, configurations are neither generated along an initial path for the transition nor equilibrated during evolution of the path. Second, and most importantly, the powerful sampling provided by the ABP serves to accelerate the dynamics during the optimization and computation of the free energy. Finally, the free energy is formulated as a potential of mean force that captures changes in the reaction channel along the principal curve, in contrast to the free energy profile evaluated from the local free-energy gradient in restrained path optimization methods. We first demonstrate the ABP formulation of path optimization using a two-dimensional potential surface and then with a more complex system of Src protein tyrosine kinase. The method is shown to be efficient and robust in the case of rugged, free-energy landscapes.
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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.