Peptide and protein docking

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

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

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

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

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

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

Increased sequence conservation of domain repeats in prokaryotic proteins. Trends Genet.

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

Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol.

Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol.


More...

Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70). Sci Rep.