PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
TLDR
PEP-FOLD3 is a novel computational framework that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance.Abstract:
Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3A from the experimental conformation and return a native-like pose in the first 10 clusters for 52% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.read more
Citations
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HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.
TL;DR: HPEPDOCK is a novel web server for blind protein–peptide docking through a hierarchical algorithm that considers the peptide flexibility through an ensemble of peptide conformations generated by the authors' MODPEP program.
Journal ArticleDOI
Targeting Aquaporin-4 Subcellular Localization to Treat Central Nervous System Edema
Philip Kitchen,Mootaz M. Salman,Mootaz M. Salman,Mootaz M. Salman,Andrea M. Halsey,Charlotte Clarke-Bland,Justin A. MacDonald,Hiroaki Ishida,Hans J. Vogel,Sharif Almutiri,Sharif Almutiri,Ann Logan,Stefan Kreida,Tamim Al-Jubair,Julie Winkel Missel,Pontus Gourdon,Pontus Gourdon,Susanna Törnroth-Horsefield,Matthew T. Conner,Zubair Ahmed,Alex C. Conner,Roslyn M. Bill +21 more
TL;DR: It is shown that AQP4 cell-surface abundance increases in response to hypoxia-induced cell swelling in a calmodulin-dependent manner, and it is proposed that targeting the mechanism of cal modulin-mediated cell- surface localization of AQP 4 is a viable strategy for development of CNS edema therapies.
Journal ArticleDOI
Protein-peptide docking: opportunities and challenges.
Maciej Pawel Ciemny,Mateusz Kurcinski,Karol Kamel,Andrzej Kolinski,Nawsad Alam,Ora Schueler-Furman,Sebastian Kmiecik +6 more
TL;DR: An overview of protein-peptide docking methods is provided and their capabilities, limitations, and applications in structure-based drug design are outlined.
Journal ArticleDOI
Whey protein hydrolysates as a source of bioactive peptides for functional foods – Biotechnological facilitation of industrial scale-up
TL;DR: The requirements of industrial processes regarding peptide release and stability, depending on several process parameters, are summarized, and some enrichment techniques for whey-derived peptides that are potentially applicable to industry are considered.
Journal ArticleDOI
Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein–peptide complexes
TL;DR: MM/PBSA and MM/GBSA are powerful tools to predict the binding affinities and identify the correct binding poses for protein-peptide systems.
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