ReviewChemical reviews2021
Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.
Review in Chemical reviews, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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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.
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Who cites it
39 citing papers in PubMed, 97 citations in OpenAlex.
- Design of aptamer peptides for immunomodulation.Journal of enzyme inhibition and medicinal chemistry · 2026Article
- Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking.RSC medicinal chemistry · 2026Article
- Dynamics of (Hetero)aryl Motifs: An Integrative Approach To Study the Conformational Landscape in Macrocycles.Journal of the American Chemical Society · 2026Article
- Cyclic Peptides as Modulators of Protein-Protein Interactions: A Survival Guide from Discovery Platforms to AI-Driven Design.International journal of molecular sciences · 2026Review
- Deep residual learning for molecular force fields.Nature communications · 2026Article
- Overcoming LPS-mediated resistance in gram-negative pathogens: a review of LL-37 analogs and computational design strategies.Archives of microbiology · 2026Review
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- Fast Generation of Simulation-Quality Structural Ensembles of Mixed-Chirality Cyclic Peptides via Diffusion Models.Journal of chemical theory and computation · 2026Article
- StrEAMM-Thioether: Efficient Structure Prediction for Thioether-Linked Cyclic Peptides.The journal of physical chemistry. B · 2026Article
- Functional Peptide-Based Biomaterials for Pharmaceutical Application: Sequences, Mechanisms, and Optimization Strategies.Journal of functional biomaterials · 2026Review
- Permeation enhancer-induced membrane defects assist the oral absorption of peptide drugs.Nature communications · 2025Article
- Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.Journal of chemical theory and computation · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Advance in peptide-based drug development: delivery platforms, therapeutics and vaccines.Signal transduction and targeted therapy · 2025Review
- Unsupervised learning of collective variables for conformational sampling of cyclic peptides.Methods in enzymology · 2025Article
- A novel antioxidant peptide from black soybean [Frontiers in nutrition · 2025Article
- CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform.Computational and structural biotechnology journal · 2024Article
- cyclicpeptide: a Python package for cyclic peptide drug design.Briefings in bioinformatics · 2024Article
- CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning.Scientific data · 2024Article
- Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides.The journal of physical chemistry. B · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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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.