ArticleStructure (London, England : 1993)2016
ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 12 citations in OpenAlex.
- Optimization of a sarbecovirus llama nanobody-antigen binding interface via a combined computational and phage display protein engineering approach.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- Optimal selection of suitable templates in protein interface prediction.Bioinformatics (Oxford, England) · 2023Article
- Estimating the accuracy of pharmacophore-based detection of cognate receptor-ligand pairs in the immunoglobulin superfamily.Proteins · 2021Article
- Residue-based pharmacophore approaches to study protein-protein interactions.Current opinion in structural biology · 2021Review
- Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands upon G89F mutation.Current research in structural biology · 2021Article
- Redesigning HVEM Interface for Selective Binding to LIGHT, BTLA, and CD160.Structure (London, England : 1993) · 2020Article
- Article
- Computational Redesign of PD-1 Interface for PD-L1 Ligand Selectivity.Structure (London, England : 1993) · 2019Article
- Protein-protein binding supersites.PLoS computational biology · 2019Article
- Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling.Journal of chemical information and modeling · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Members of the extracellular immunoglobulin superfamily (IgSF) play a key role in immune regulation through the control of the co-stimulatory pathway, and have emerged as potent drug targets in cancers, infectious diseases, and autoimmunity. Despite the difficult experimental access to this class of proteins, single structures of ectodomains of IgSF proteins are solved with regularity. However, the most biologically critical challenge for this class of proteins is the identification of their cognate ligands that communicate intercellular signals. We describe a conceptually novel method, protein-ligand interface design (ProtLID), to identify cognate ligands from a subproteome for a given target receptor protein. ProtLID designs an optimal protein interface for a given receptor by running extensive molecular dynamics simulations of single-residue probes. The type and location of residue preferences establish a residue-based pharmacophore, which is subsequently used to find potential matches among candidate ligands within a subproteome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.