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PepCA: Unveiling Protein-Peptide Interaction Sites with a Multimodal Neural Network Model

https://doi.org/10.2139/ssrn.4800950
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design
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Sequence‐based prediction of protein–peptide binding sites using support vector machine
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From Protein Structure to Function with Bioinformatics
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Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server
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Understand protein functions by comparing the similarity of local structural environments
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Therapeutic peptides: Historical perspectives, current development trends, and future directions
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Generative design of therapeutics that bind and modulate protein states
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Protein–peptide docking: opportunities and challenges
inferredcites →https://doi.org/10.1016/j.isci.2022.105920openalex-extracted
How good are AlphaFold models for docking-based virtual screening?
inferredcites →https://doi.org/10.1016/j.jmb.2021.167208openalex-extracted
AlphaFold and Implications for Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jcim.8b00019openalex-extracted
Improving Sequence-Based Prediction of Protein–Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method
inferredcites →https://doi.org/10.1021/acs.jctc.9b01208openalex-extracted
Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes
inferredcites →https://doi.org/10.1021/ja026939xopenalex-extracted
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1038/nature11503openalex-extracted
Structure-based prediction of protein–protein interactions on a genome-wide scale
inferredcites →https://doi.org/10.1038/s41573-020-00135-8openalex-extracted
Trends in peptide drug discovery
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-extracted
Highly accurate protein structure prediction with AlphaFold
inferredcites →https://doi.org/10.1038/s41594-021-00714-2openalex-extracted
Can AlphaFold2 predict the impact of missense mutations on structure?
inferredcites →https://doi.org/10.1038/s41598-019-38498-7openalex-extracted
Predicting protein-peptide interaction sites using distant protein complexes as structural templates
inferredcites →https://doi.org/10.1038/s42003-022-03445-2openalex-extracted
PepNN: a deep attention model for the identification of peptide binding sites
inferredcites →https://doi.org/10.1038/s42003-023-05464-zopenalex-extracted
SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders
inferredcites →https://doi.org/10.1093/bioinformatics/btac352openalex-extracted
Predicting protein–peptide binding residues via interpretable deep learning
inferredcites →https://doi.org/10.1093/bioinformatics/btad646openalex-extracted
THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model
inferredcites →https://doi.org/10.1093/bioinformatics/btad718openalex-extracted
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model
inferredcites →https://doi.org/10.1093/bioinformatics/btx614openalex-extracted
Structure-based prediction of protein– peptide binding regions using Random Forest
inferredcites →https://doi.org/10.1093/nar/gks398openalex-extracted
PepSite: prediction of peptide-binding sites from protein surfaces
inferredcites →https://doi.org/10.1093/nar/gku1028openalex-extracted
A series of PDB-related databanks for everyday needs
inferredcites →https://doi.org/10.1093/nar/gku404openalex-extracted
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
inferredcites →https://doi.org/10.1126/science.1083653openalex-extracted
Assembly of Cell Regulatory Systems Through Protein Interaction Domains
inferredcites →https://doi.org/10.1126/science.ade2574openalex-extracted
Evolutionary-scale prediction of atomic-level protein structure with a language model
inferredcites →https://doi.org/10.1186/s12859-018-2449-yopenalex-extracted
Benchmarking of different molecular docking methods for protein-peptide docking
inferredcites →https://doi.org/10.1371/journal.pone.0018934openalex-extracted
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors
inferredcites →https://doi.org/10.17863/cam.48429openalex-extracted
Graph Attention Networks
inferredcites →https://doi.org/10.3389/fbinf.2023.1120370openalex-extracted
Before and after AlphaFold2: An overview of protein structure prediction
inferredcites →https://doi.org/10.3390/biom12070985openalex-extracted
Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction
inferredcites →https://doi.org/10.3390/ijms20102383openalex-extracted
A Comprehensive Review on Current Advances in Peptide Drug Development and Design
inferredcites →https://doi.org/10.48550/arxiv.1611.01604openalex-extracted
Dynamic Coattention Networks For Question Answering
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