ArticleBiology direct2015
PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues.
Article in Biology direct, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers, 1 of them a synthesis that pooled it.
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Who cites it
99 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Roles of d-Amino Acids on the Bioactivity of Host Defense Peptides.International journal of molecular sciences · 2016Pooled it
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- Assessment of molecular interactions and anti-inflammatory activity of fermented camel milk-derived peptides in RAW macrophages.Amino acids · 2026Article
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- Prediction of Chemically Modified Antimicrobial Peptides and Their Sub-functional Activities Using Hybrid Features.Probiotics and antimicrobial proteins · 2026Article
- Advances in cyclotide research: bioactivity to cyclotide-based therapeutics.Molecular diversity · 2025Review
- A comprehensive dataset of therapeutic peptides on multi-function property and structure information.Scientific data · 2025Article
- CancerPPD2: an updated repository of anticancer peptides and proteins.Database : the journal of biological databases and curation · 2025Article
- Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2.Briefings in bioinformatics · 2025Article
- Identification and inhibition of PIN1-NRF2 protein-protein interactions through computational and biophysical approaches.Scientific reports · 2025Article
- Cellular Activity of CQWW Nullomer-Derived Peptides.ACS omega · 2025Article
- Structural information in therapeutic peptides: Emerging applications in biomedicine.FEBS open bio · 2025Review
- Food-derived linear vs. rationally designed cyclic peptides as potent TNF-alpha inhibitors: an integrative computational study.Frontiers in bioinformatics · 2025Article
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- Computational investigation of antiviral peptide interactions with Mpox DNA polymerase.In silico pharmacology · 2025Article
- Characterization and preparation of food-derived peptides on improving osteoporosis: A review.Food chemistry: X · 2024Article
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39 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
backgroundIn the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natural and non-natural/modified residues.
resultsPEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER. AMBER was also used to handle other modifications like peptide cyclization, use of D-amino acids and capping of terminal residues. In addition, GROMACS was used to implement 210 non-natural side-chains in peptides using SwissSideChain force field library. We evaluated the performance of PEPstrMOD on three datasets generated from Protein Data Bank; i) ModPep dataset contains 501 non-natural peptides, ii) ModPep16, a subset of ModPep, and iii) CyclicPep contains 34 cyclic peptides. We achieved backbone Root Mean Square Deviation between the actual and predicted structure of peptides in the range of 3.81-4.05 Å.
conclusionsIn summary, the method PEPstrMOD has been developed that predicts the structure of modified peptide from the sequence/structure given as input. We validated the PEPstrMOD application using a dataset of peptides having non-natural/modified residues. PEPstrMOD offers unique advantages that allow the users to predict the structures of peptides having i) natural residues, ii) non-naturally modified residues, iii) terminal modifications, iv) post-translational modifications, v) D-amino acids, and also allows extended simulation of predicted peptides. This will help the researchers to have prior structural information of modified peptides to further design the peptides for desired therapeutic property. PEPstrMOD is freely available at http://osddlinux.osdd.net/raghava/pepstrmod/.
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