ArticleJournal of chemical theory and computation2016
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- FakeRotLib: Expedient Noncanonical Amino Acid Parametrization in Rosetta.Journal of chemical information and modeling · 2025Article
- Machine-learned molecular mechanics force fields from large-scale quantum chemical data.Chemical science · 2024Article
- Article
- Determining the Predominant Conformations of Mortiamides A-D in Solution Using NMR Data and Molecular Modeling Tools.ACS omega · 2023Article
- NUMERICALLY STABLE SOLUTION TO THE 6R PROBLEM OF INVERSE KINEMATICS.Advances in computational science and engineering · 2023Article
- Beyond 20 in the 21st Century: Prospects and Challenges of Non-canonical Amino Acids in Peptide Drug Discovery.ACS medicinal chemistry letters · 2023Review
- Kinematic Reconstruction of Cyclic Peptides and Protein Backbones from Partial Data.Journal of chemical information and modeling · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Benchmark of Generic Shapes for Macrocycles.Journal of chemical information and modeling · 2020Article
- Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments.Journal of chemical information and modeling · 2020Article
- Conformational analysis of macrocycles: comparing general and specialized methods.Journal of computer-aided molecular design · 2020Article
- D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Journal of computer-aided molecular design · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study.ACS omega · 2019Article
- Conformation and Permeability: Cyclic Hexapeptide Diastereomers.Journal of chemical information and modeling · 2019Article
- Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock.Journal of molecular modeling · 2019Article
- Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.Journal of computer-aided molecular design · 2019Article
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?ACS omega · 2018Article
- Artificial Macrocycles.Synlett : accounts and rapid communications in synthetic organic chemistry · 2018Article
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Authors and funding
5 authors.
Funding
Abstract
Natural product and synthetic macrocycles are chemically and topologically diverse. An efficient, accurate, and general method for generating macrocycle conformations would enable structure-based design of macrocycle drugs or host-guest complexes. Computational sampling also provides insight into transiently populated states, complementing crystallographic and NMR data. Here, we report a new algorithm, BRIKARD, that addresses this challenge through computational algebraic geometry and inverse kinematics together with local energy minimization. BRIKARD is demonstrated on 67 diverse macrocycles with structural data, encompassing various ring topologies. We find this approach enumerates diverse structures with macrocyclic RMSD < 1.0 Å to the experimental conformation for 85% of our data set in contrast to success rates of 67-75% with other approaches, while for the subset of 21 more challenging compounds in the data set, these rates are 57% and 10-29%, respectively. Because the algorithm can be efficiently run in parallel on many processors, exhaustive conformational sampling of complex cycles can be obtained in minutes rather than hours: with a 40 processor implementation protocol, BRIKARD samples the conformational diversity of a potential energy landscape in a median of 1.3 minutes of wallclock time, much faster than 3.1-10.3 hours necessary with current programs. By rigorously testing BRIKARD on a broad range of scaffolds with highly complex ring systems, we push the frontiers of macrocycle sampling to encompass multiring compounds, including those with more than 50 ring atoms and up to seven interlaced flexible rings.
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Registered trials
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