ArticleJournal of computer-aided molecular design2020
Conformational analysis of macrocycles: comparing general and specialized methods.
Article in Journal of computer-aided molecular design, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Structure-based design of subtype-selective psychedelic analogs.Nature communications · 2026Article
- Macropa Scaffold Expansion for Actinium-225 Chelation: A Synthetic Strategy, Labeling Kinetics, and Theoretical Calculations.Inorganic chemistry · 2026Article
- Article
- Rational Activity Improvement of Cyclic Peptides through Stabilization and Rigidification of Main Chain Using φ/ψ Plots of Amino Acids.ACS omega · 2025Article
- Macrocyclic Aromatic Oligoamides with Diphenyladamantane Units: Conformational Change from Folded to Open by N-Alkyl Removal.Molecules (Basel, Switzerland) · 2025Article
- Vincristine Beyond Mitosis: Uncovering a First Link to G-Quadruplex DNA in Cancer Cells.International journal of molecular sciences · 2025Article
- Application of Free Energy Perturbation (FEP) Methodology for Predicting the Binding Affinity of Macrocyclic JAK2 Inhibitor Analogues of Pacritinib.ACS medicinal chemistry letters · 2025Article
- Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs).Nature communications · 2024Article
- Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.Journal of chemical information and modeling · 2023Article
- High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment.Journal of chemical information and modeling · 2023Article
- Using Macrocyclic G-Quadruplex Ligands to Decipher the Interactions Between Small Molecules and G-Quadruplex DNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Benchmark of Generic Shapes for Macrocycles.Journal of chemical information and modeling · 2020Article
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Authors and funding
4 authors.
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Abstract
Macrocycles represent an important class of medicinally relevant small molecules due to their interesting biological properties. Therefore, a firm understanding of their conformational preferences is important for drug design. Given the importance of macrocycle-protein modelling in drug discovery, we envisaged that a systematic study of both classical and recent specialized methods would provide guidance for other practitioners within the field. In this study we compare the performance of the general, well established conformational analysis methods Monte Carlo Multiple Minimum (MCMM) and Mixed Torsional/Low-Mode sampling (MTLMOD) with two more recent and specialized macrocycle sampling techniques: MacroModel macrocycle Baseline Search (MD/LLMOD) and Prime macrocycle conformational sampling (PRIME-MCS). Using macrocycles extracted from 44 macrocycle-protein X-ray crystallography complexes, we evaluated each method based on their ability to (i) generate unique conformers, (ii) generate unique macrocycle ring conformations, (iii) identify the global energy minimum, (iv) identify conformers similar to the X-ray ligand conformation after Protein Preparation Wizard treatment (X-ray
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