ArticleACS synthetic biology2014
Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.
Article in ACS synthetic biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- HighFold-MeD: a Rosetta distillation model to accelerate structure prediction of cyclic peptides with backbone N-methylation and D-amino acids.Journal of cheminformatics · 2025Article
- Artificial Intelligence Transforming Post-Translational Modification Research.Bioengineering (Basel, Switzerland) · 2024Review
- AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank.International journal of molecular sciences · 2024Article
- Synthesis, biological evaluation and metadynamics simulations of novelRSC medicinal chemistry · 2024Article
- Accurate estimates of dynamical statistics using memory.The Journal of chemical physics · 2024Article
- Structural dynamics influences the antibacterial activity of a cell-penetrating peptide (KFF)Scientific reports · 2023Article
- Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.The Journal of chemical physics · 2023Article
- On the plasticity of amyloid formation: The impact of destabilizing small to large substitutions on islet amyloid polypeptide amyloid formation.Protein science : a publication of the Protein Society · 2023Article
- Engineering of enzymes using non-natural amino acids.Bioscience reports · 2022Review
- Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau FragmentInternational journal of molecular sciences · 2022Article
- A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality.Frontiers in bioengineering and biotechnology · 2022Article
- Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions.Frontiers in molecular biosciences · 2022Article
- An allosteric regulation mechanism of Arabidopsis Serine/Threonine kinase 1 (SIK1) through phosphorylation.Computational and structural biotechnology journal · 2022Article
- Cyclosporin A: Conformational Complexity and Chameleonicity.Journal of chemical information and modeling · 2021Article
- Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine.Scientific reports · 2021Article
- A predictive coarse-grained model for position-specific effects of post-translational modifications.Biophysical journal · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
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6 authors.
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Abstract
We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA . The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions.
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