ArticleNature communications2017
Finding multiple reaction pathways via global optimization of action.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- MOZAIC: compound growth via in silico reactions and global optimization using Conformational Space Annealing.Bioinformatics (Oxford, England) · 2026Article
- Following the Committor Flow: A Data-Driven Discovery of Transition Pathways.Journal of chemical theory and computation · 2026Article
- MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization.Nucleic acids research · 2024Article
- Residues L55 and W69 of Tva Mediate Entry of Subgroup A Avian Leukosis Virus.Journal of virology · 2022Article
- MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization.ACS omega · 2021Article
- Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning.JACS Au · 2021Review
- MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES.Journal of cheminformatics · 2021Article
- Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T.The journal of physical chemistry letters · 2020Article
- Hierarchical Markov State Model Building to Describe Molecular Processes.Journal of chemical theory and computation · 2020Article
- Non-sequential protein structure alignment by conformational space annealing and local refinement.PloS one · 2019Article
- Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.International journal of molecular sciences · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways. The rank order and the transition time distribution of multiple pathways are in good agreement with those of long Langevin dynamics simulations. The lowest action folding pathway of FSD-1 is consistent with recent experiments. The results show that Action-CSA is an efficient and robust computational approach to study the multiple pathways of complex reactions and large-scale conformational changes.
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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.