ArticleMethods in molecular biology (Clifton, N.J.)2016
Rosetta and the Design of Ligand Binding Sites.
Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed, 41 citations in OpenAlex.
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- Potential C-terminal domain interactions of the cardiac voltage gated sodium channel.Scientific reports · 2025Article
- Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan.Journal of structural biology · 2025Article
- Identification and Optimization of more Efficient Olivetolic Acid Synthases.Cannabis and cannabinoid research · 2024Article
- Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain.ACS chemical neuroscience · 2024Article
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase.Nature communications · 2022Article
- A Comparative Study between Spanish and British SARS-CoV-2 Variants.Current issues in molecular biology · 2021Article
- Computational redesign of a fluorogen activating protein with Rosetta.PLoS computational biology · 2021Article
- Interface-based design of the favipiravir-binding site in SARS-CoV-2 RNA-dependent RNA polymerase reveals mutations conferring resistance to chain termination.FEBS letters · 2021Article
- High-throughput rational design of the remdesivir binding site in the RdRp of SARS-CoV-2: implications for potential resistance.iScience · 2021Article
- Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit.Physical chemistry chemical physics : PCCP · 2018Article
- Design of a heme-binding peptide motif adopting a β-hairpin conformation.The Journal of biological chemistry · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Proteins that bind small molecules (ligands) can be used as biosensors, signal modulators, and sequestering agents. When naturally occurring proteins for a particular target ligand are not available, artificial proteins can be computationally designed. We present a protocol based on RosettaLigand to redesign an existing protein pocket to bind a target ligand. Starting with a protein structure and the structure of the ligand, Rosetta can optimize both the placement of the ligand in the pocket and the identity and conformation of the surrounding sidechains, yielding proteins that bind the target compound.
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Registered trials
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