ArticlePloS one2015
In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Repositioning Antimicrobial Peptides Against WHO-Priority Fungi.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Designing microplastic-binding peptides with a variational quantum circuit-based hybrid quantum-classical approach.Science advances · 2024Article
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors.International journal of molecular sciences · 2021Article
- Proteomimetics of Natural Regulators of JAK-STAT Pathway: Novel Therapeutic Perspectives.Frontiers in molecular biosciences · 2021Review
- Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2.Advanced theory and simulations · 2020Article
- Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches.Antibiotics (Basel, Switzerland) · 2020Review
- Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2.ChemRxiv : the preprint server for chemistry · 2020Article
- In silico design of peptides as potential ligands to resistin.Journal of molecular modeling · 2020Article
- Homology Modeling-Based in Silico Affinity Maturation Improves the Affinity of a Nanobody.International journal of molecular sciences · 2019Article
- Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.BMC bioinformatics · 2017Article
- Unique Footprint in the scl1.3 Locus Affects Adhesion and Biofilm Formation of the Invasive M3-Type Group A Streptococcus.Frontiers in cellular and infection microbiology · 2016Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
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