PEP-FOLD: an online resource for de novo peptide structure prediction

Maupetit, Julien; Derreumaux, Philippe; Tufféry, Pierre

doi:10.1093/nar/gkp323

Cited by 360 publications

(337 citation statements)

References 29 publications

(42 reference statements)

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“…The specific peptides were selected based on (i) having a high MS identification score, and (ii) the WebLogos in the sense that they should contain the refined binding motif(s), but still displaying large sequence differences upstream of the refined motif including the N-terminal. The peptides were modeled using mainly PEP-FOLD, 37 but also PROFASI. 38 The peptide-antibody complexes were modeled using PRO-FASI, and to ensure that we did not introduce a bias in the peptide modeling, we performed dual modeling of the peptides.…”

Section: Structural Analysis Of Peptidesmentioning

confidence: 99%

Epitope‐specificity of recombinant antibodies reveals promiscuous peptide‐binding properties

et al. 2012

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Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibodypeptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.

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Section: Structural Analysis Of Peptidesmentioning

confidence: 99%

Epitope‐specificity of recombinant antibodies reveals promiscuous peptide‐binding properties

et al. 2012

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“…The amino acid sequences of PreS1 and PreS2 1-11 domains were obtained from UniProtKB Swiss-Prot database [33] (UniProt Entry: P03141). These sequences were then used for De Novo prediction of 3D structures in Pep-Fold server [16]. The amino acid sequence of NTCP was also obtained from UniProtKB SwissProt database (UniProt Entry: Q12908) and used in for homology based 3D structure prediction RaptorX server [24].…”

Section: Methodsmentioning

confidence: 99%

Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors

Mohebbi¹,

Mohammadi

Memarian

2016

VirusDis.

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Hepatitis B virus (HBV) is an etiological agent of viral hepatitis, which may lead to cirrhosis, and hepatocellular carcinoma. Current treatment strategies have not shown promising effect to date but various complications such as, drug toxicity-resistance have been reported. Study on newly discovered compounds, with minimal side effects, as specific HBV inhibitors is a fundamental subject introducing new biologic drugs. Here, we aimed to, by prediction, estimate interactions of HBF-0259 as a nontoxic anti-HBV compound on inhibiting the HBV through either interaction with the viral entry or HBsAg secreting factors using In Silico procedure. Molecular docking was performed by Hex 8.0.0 software to predict the interaction energy (Etot) between HBF-0259 and known cellular factors involved in HBV entry and HBsAg secreting factors. Hex 8.0.0 also employed to create protein-protein complexes. These interactions were then used to analyze the binding site of HBF-0259 within the assumed receptors by MGLTools software. Finally, the amino acid sequences involved in this interaction were aligned for any conservancy. Here, we showed that HBF-0259 Etot with CypA (-545.41 kcal/mol) and SCCA1 (499.68 kcal/mol), involved in HBsAg secretion and HBV integration, respectively, was higher than other interactions. Furthermore, HBF-0259 predicted interaction energy was even higher than those of CypA inhibitors. In addition, we claim that preS1 and/or preS2 regions within HBsAg are not suitable targets for HBF-0259. HBF-0259 has higher interaction energy with CypA and SCCA1, even more than other known receptors, co-receptors, viral ligands, and secretory factors. HBF-0259 could be introduced as potent anti-viral compound in which CypA and or SCCA1, as previously shown, are involved.

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“…Model of Vt3.1-The structure of a monomeric Vt3.1 peptide was generated by using PEP-FOLD, a de novo structure prediction server (21), which was then optimized by long time scale molecular dynamics simulations using the NAMD program (version 2.9) (22).…”

Section: Methodsmentioning

confidence: 99%

Conopeptide Vt3.1 Preferentially Inhibits BK Potassium Channels Containing β4 Subunits via Electrostatic Interactions

Chang

Yang

et al. 2014

Journal of Biological Chemistry

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Background: BK channel function is differentially modulated by tissue-specific ␤ (␤1-4) subunits. Results: Conopeptide Vt3.1 preferentially inhibits neuronal BK channels containing the ␤4 subunit. Conclusion: Electrostatic interactions between Vt3.1 and the extracellular loop of ␤4 decrease voltage-dependent activation of the channel. Significance: Vt3.1 is an excellent tool for studying the structure, function, and roles in neurophysiology of BK channels.

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PEP-FOLD: an online resource for de novo peptide structure prediction

Cited by 360 publications

References 29 publications

Epitope‐specificity of recombinant antibodies reveals promiscuous peptide‐binding properties

Epitope‐specificity of recombinant antibodies reveals promiscuous peptide‐binding properties

Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors

Conopeptide Vt3.1 Preferentially Inhibits BK Potassium Channels Containing β4 Subunits via Electrostatic Interactions

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