ArticleThe journal of physical chemistry. B2018
Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking.RSC medicinal chemistry · 2026Article
- Cooperative Oligomeric Peptide Combinations Enhance the Predicted Therapeutic Profile of SET-M33.Antibiotics (Basel, Switzerland) · 2026Article
- StrEAMM-Thioether: Efficient Structure Prediction for Thioether-Linked Cyclic Peptides.The journal of physical chemistry. B · 2026Article
- Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.Journal of chemical theory and computation · 2025Article
- Development of Next Generation Cell-Permeable Peptide Inhibitors for the Oncological Target MAGE-A4.Journal of medicinal chemistry · 2025Article
- Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?Journal of chemical information and modeling · 2025Article
- Unsupervised learning of collective variables for conformational sampling of cyclic peptides.Methods in enzymology · 2025Article
- Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics.Chemical reviews · 2024Review
- Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides.The journal of physical chemistry. B · 2024Article
- Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.Journal of chemical information and modeling · 2023Article
- Training Neural Network Models Using Molecular Dynamics Simulation Results to Efficiently Predict Cyclic Hexapeptide Structural Ensembles.Journal of chemical theory and computation · 2023Article
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Structure prediction of cyclic peptides by molecular dynamics + machine learning.Chemical science · 2021Article
- CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting.Journal of chemical information and modeling · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Cyclic peptides: backbone rigidification and capability of mimicking motifs at protein-protein interfaces.Physical chemistry chemical physics : PCCP · 2021Article
- Computational design of mixed chirality peptide macrocycles with internal symmetry.Protein science : a publication of the Protein Society · 2020Article
- An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.Nucleic acids research · 2019Article
- β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides.Biophysical journal · 2019Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Cyclic peptides are a promising class of molecules for unique applications. Unfortunately, cyclic peptide design is severely limited by the difficulty in predicting the conformations they will adopt in solution. In this work, we use explicit-solvent molecular dynamics simulations to design well-structured cyclic peptides by studying their sequence-structure relationships. Critical to our approach is an enhanced sampling method that exploits the essential transitional motions of cyclic peptides to efficiently sample their conformational space. We simulated a range of cyclic pentapeptides from all-glycine to a library of cyclo-(X
Indexed as
Identifiers
What OpenQuestion holds
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.