Peptide and protein docking
Peptide and protein docking
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Lee*, Hubrich*, Varga*, Schäfer, Welzel, Schumbera, Đokić, Morgan Strom, Schönfeld, Geist, Polat, Gibson, Keller Valsecchi, Kumar, Schueler-Furman#, Luck# (2023)
Lee*, Hubrich*, Varga*, Schäfer, Welzel, Schumbera, Đokić, Morgan Strom, Schönfeld, Geist, Polat, Gibson, Keller Valsecchi, Kumar, Schueler-Furman#, Luck# (2023)
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Accepted for publication in Molecular Systems Biology
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Accepted for publication in Molecular Systems Biology
Structural study of UFL1‐UFC1 interaction uncovers the role of UFL1 N‐terminal helix in ufmylation. EMBO Reports
Protein language models can capture protein quaternary state. BMC Bioinformatics
Protein language models can capture protein quaternary state. BMC Bioinformatics
Elucidation of Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains. Biochemistry
Elucidation of Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains. Biochemistry
Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study. Proteomics
Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study. Proteomics
Systemic structural analysis of alterations reveals a common structural basis of driver mutations in cancer. NAR Cancer
Systemic structural analysis of alterations reveals a common structural basis of driver mutations in cancer. NAR Cancer
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nature Biotechnology
Harnessing protein folding neural networks for peptide–protein docking. Nature Communications
Khramushin, Ben-Aharon, Tsaban, Varga, Avraham & Schueler-Furman (2022)
Matching protein surface structural patches for high-resolution blind peptide docking. PNAS
Rotem-Bamberger, Fahoum, Keinan-Adamsky, Tsaban, Avraham, Shalev, Chill, Schueler-Furman (2022)
Structural insights into the role of the WW2 domain on tandem WW–PPxY motif interactions of oxidoreductase WWOX. JBC
Varga*, Diffley*, Welker Leng, Fierke, Schueler-Furman (2022)
Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. Scientific Reports
Structural basis for UFM1 transfer from UBA5 to UFC1. Nature Communications
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45. Proteins: Structure, Function, and Bioinformatics.
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Comput Biol.
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinformatics
Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol.
Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server. Methods Mol Biol.
FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins.
A benchmark testing ground for integrating homology modeling and protein docking. Proteins.
Rosetta FlexPepDock web server-high resolution modeling of peptide-protein interactions.Nucleic Acids Res.
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors. PLoS One.
The structural basis of peptide-protein binding strategies. Structure.
Reviews and books
Reviews and books
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures. Protein Structure Prediction.
Protein-peptide docking: opportunities and challenges. Drug Discov Today.
Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol.
Druggable protein-protein interactions-from hot spots to hot segments. Curr Opin Chem Biol.
Binding specificity and design
Binding specificity and design
Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. Scientific reports
Structure-Based Identification of HDAC8 Non-histone Substrates. Structure.
Crucial roles of single residues in binding affinity, specificity and promiscuity in the cellulosomal cohesin-dockerin interface. JBC.
Rationally Designed Macrocyclic Peptides as Synergistic Agonists of LPS-Induced Inflammatory Response. Tetrahedron.
Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PLoS Comput Biol.
Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm. Trends Microbiol.
Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm. Trends Microbiol.
Derived peptides
Derived peptides
Peptiderive server: derive peptide inhibitors from protein-protein interactions. Nucleic Acids Res.
Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins.
Peptide-protein interactions within their context
Peptide-protein interactions within their context
Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite. Cell Chem Biol.
Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors. Front Cell Infect Microbiol.
Versatile communication strategies among tandem WW domain repeats. Exp Biol Med 240:351-360.
The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK. Mol Cell.
Structural impact of mutations
Structural impact of mutations
MYORG is associated with recessive primary familial brain calcification. Ann Clin Transl Neurol.
Molecular pathogenesis of human CD59 deficiency. Neurol Genet.
Parkin Somatic Mutations Link Melanoma and Parkinson's Disease. J Genet Genomics.
Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells. J Biol Chem.
Evolution of domain repeats
Evolution of domain repeats
Increased sequence conservation of domain repeats in prokaryotic proteins. Trends Genet.
Energy landscapes
Energy landscapes
Encounter complexes and dimensionality reduction in protein-protein association. Elife.
FunHunt: model selection based on energy landscape characteristics. Biochem Soc Trans.
Protein Motion
Protein Motion
Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol.
Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol.
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Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70). Sci Rep.
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