ArticleNucleic acids research2023
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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80 citing papers in PubMed.
- Countering postoperative immune suppression with a self-assembling dendritic cell nanovaccine.Bioactive materials · 2026Article
- Peptidomics-guided 3D structural-mechanistic investigation of bovine colostrum peptides reveals multi-targetedFood chemistry: X · 2026Article
- Comparative Genomics-Guided Epitope Prioritization and in Silico Design of a Multi-Epitope DNA Vaccine Candidate Against Megalocytivirus pagrus 1.Marine biotechnology (New York, N.Y.) · 2026Article
- Ammonification Process Is Limited by Transformation of Medium Molecular Weight Nitrogenous Organics but Not Hydrolysis of Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cnidarian Venoms in the Omics Era: Toxin Discovery and Bioactive Potential.Marine drugs · 2026Review
- UniPept: A Universal Model for Predicting Peptide Properties Based on Atom-Residue Dual-Scale Integration.Interdisciplinary sciences, computational life sciences · 2026Article
- Mechanism-Informed Machine Learning Enables Discovery of Oncolytic Peptides for Cancer Immunotherapy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Optimization of CEST MRI Reporter Protein Design Using Cation-Pi Networks.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Article
- PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides.Nucleic acids research · 2026Article
- DeepPepQSAR: all-in-one for comprehensively exploiting the vast molecular diversity space of bioactive peptide universe.Molecular diversity · 2026Article
- Engineering a high-affinity multiple antigenic peptide dendrimer for group-specific detection of bluetongue virus antibodies targeting the VP7 epitope.Molecular biology reports · 2026Article
- Venom-Derived Enzyme Inhibitors as Anticancer Agents: Structure-Activity Relationships, Molecular Targets and Mechanistic Insights.Molecules (Basel, Switzerland) · 2026Review
- Discovery of potent low-toxicity antimicrobial peptides through diffusion modeling.Nature communications · 2026Article
- Combining Fret and Super-Resolution Microscopy Reveals Kinase Activation and Mitochondrial Activity at the Nanoscale.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An immune-associated mitochondrial DNA variant with sex differences reveals a putative novel microprotein called MASL.Immunity & ageing : I & A · 2026Article
- A peptide-induced regression of low-grade malignant breast tumor via activation of autophagy in breast cancer cells.Molecular medicine (Cambridge, Mass.) · 2026Article
- Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery.PLoS computational biology · 2026Article
- Beyond formic acid: Peptides in carpenter ant venoms aid in disease protection.Science advances · 2026Article
- Antimicrobial Potential of Defensin-DerivedInternational journal of molecular sciences · 2026Article
20 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution has many biological applications, but their conformations are pH- and salt concentration-dependent. In this work, we present PEP-FOLD4 which goes one step beyond many machine-learning approaches, such as AlphaFold2, TrRosetta and RaptorX. Adding the Debye-Hueckel formalism for charged-charged side chain interactions to a Mie formalism for all intramolecular (backbone and side chain) interactions, PEP-FOLD4, based on a coarse-grained representation of the peptides, performs as well as machine-learning methods on well-structured peptides, but displays significant improvements for poly-charged peptides. PEP-FOLD4 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4. This server is free and there is no login requirement.
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