ArticleJournal of chemical theory and computation2011
Assessing protein loop flexibility by hierarchical Monte Carlo sampling.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 24 citations in OpenAlex.
- In silico drug repurposing of potential antiviral inhibitors targeting methyltransferase (2'-O-MTase) domain of Marburg virus.In silico pharmacology · 2025Article
- Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme.Microorganisms · 2020Article
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods.Molecules (Basel, Switzerland) · 2018Article
- Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops.Journal of chemical theory and computation · 2017Article
- Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.Journal of chemical theory and computation · 2016Article
- Force distribution in a semiflexible loop.Physical review. E · 2016Article
- Constraint methods that accelerate free-energy simulations of biomolecules.The Journal of chemical physics · 2015Review
- Conformational sampling in template-free protein loop structure modeling: an overview.Computational and structural biotechnology journal · 2013Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Loop flexibility is often crucial to protein biological function in solution. We report a new Monte Carlo method for generating conformational ensembles for protein loops and cyclic peptides. The approach incorporates the triaxial loop closure method which addresses the inverse kinematic problem for generating backbone move sets that do not break the loop. Sidechains are sampled together with the backbone in a hierarchical way, making it possible to make large moves that cross energy barriers. As an initial application, we apply the method to the flexible loop in triosephosphate isomerase that caps the active site, and demonstrate that the resulting loop ensembles agree well with key observations from previous structural studies. We also demonstrate, with 3 other test cases, the ability to distinguish relatively flexible and rigid loops within the same protein.
Identifiers
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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.