ArticleJournal of biomolecular NMR2015
NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Streamlined Postprocessing of NMR Structures with the Molecular Restrainer: A Universal Tool for High-Quality Protein-Ligand Models and Non-Standard Amino Acid Residues.International journal of molecular sciences · 2025Article
- Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.Journal of computer-aided molecular design · 2023Article
- Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations.The journal of physical chemistry. A · 2023Article
- Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP.Communications biology · 2023Article
- Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.Magnetic resonance (Gottingen, Germany) · 2023Article
- The occurrence of ansamers in the synthesis of cyclic peptides.Nature communications · 2022Article
- Article
- Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability.Organic letters · 2022Article
- Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Structure-Activity Relationship Investigations of Novel Constrained Chimeric Peptidomimetics of SOCS3 Protein Targeting JAK2.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Protein-ligand structure determination with the NMR molecular replacement tool, NMRJournal of biomolecular NMR · 2020Article
- Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3The Journal of organic chemistry · 2020Article
- Directed Evolution Using Stabilized Bacterial Peptide Display.Journal of the American Chemical Society · 2020Article
- A genetics-free method for high-throughput discovery of cryptic microbial metabolites.Nature chemical biology · 2019Article
- Structural studies suggest aggregation as one of the modes of action for teixobactin.Chemical science · 2018Article
- High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.Communications biology · 2018Article
- The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.Communications biology · 2018Article
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2 authors.
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Abstract
An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.
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