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Deciphering interaction fingerprints from protein molecular surfaces

https://doi.org/10.1101/606202
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
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Prediction‐based fingerprints of protein–protein interactions
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Efficient Unbound Docking of Rigid Molecules
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A simple method for displaying the hydropathic character of a protein
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Rosetta3
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Crystal Structure of d-Erythronate-4-phosphate Dehydrogenase Complexed with NAD
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Understanding Protein–Protein Interactions Using Local Structural Features
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Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
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Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1
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An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
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Structure-based prediction of protein–protein interactions on a genome-wide scale
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Computational design of ligand-binding proteins with high affinity and selectivity
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Proof of principle for epitope-focused vaccine design
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The coming of age of de novo protein design
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The I-TASSER Suite: protein structure and function prediction
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The Phyre2 web portal for protein modeling, prediction and analysis
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Coordination of microbial metabolism
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Computational redesign of protein-protein interaction specificity
inferredcites →https://doi.org/10.1073/pnas.0906146106openalex-snapshot
Fast screening of protein surfaces using geometric invariant fingerprints
inferredcites →https://doi.org/10.1073/pnas.181342398openalex-snapshot
Electrostatics of nanosystems: Application to microtubules and the ribosome
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The Crystal Structure of Six-transmembrane Epithelial Antigen of the Prostate 4 (Steap4), a Ferri/Cuprireductase, Suggests a Novel Interdomain Flavin-binding Site
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu626openalex-snapshot
PDB-wide collection of binding data: current status of the PDBbind database
inferredcites →https://doi.org/10.1093/bioinformatics/btu724openalex-snapshot
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0
inferredcites →https://doi.org/10.1093/bioinformatics/btx585openalex-snapshot
IntPred: a structure-based predictor of protein–protein interaction sites
inferredcites →https://doi.org/10.1093/bioinformatics/bty918openalex-snapshot
Antibody interface prediction with 3D Zernike descriptors and SVM
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TM-align: a protein structure alignment algorithm based on the TM-score
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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
inferredcites →https://doi.org/10.1093/nar/gkt1043openalex-snapshot
SAbDab: the structural antibody database
inferredcites →https://doi.org/10.1093/nar/gku397openalex-snapshot
PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes
inferredcites →https://doi.org/10.1109/cvpr.2017.576openalex-snapshot
Geometric Deep Learning on Graphs and Manifolds Using Mixture Model CNNs
inferredcites →https://doi.org/10.1109/iccvw.2015.112openalex-snapshot
Geodesic Convolutional Neural Networks on Riemannian Manifolds
inferredcites →https://doi.org/10.1109/icpr.2016.7900298openalex-snapshot
Palmprint recognition via discriminative index learning
inferredcites →https://doi.org/10.1109/msp.2017.2693418openalex-snapshot
Geometric Deep Learning: Going beyond Euclidean data
inferredcites →https://doi.org/10.1109/tpami.2014.2321376openalex-snapshot
Scalable Nearest Neighbor Algorithms for High Dimensional Data
inferredcites →https://doi.org/10.1111/j.1745-3984.2003.tb01108.xopenalex-snapshot
Modern Multidimensional Scaling: Theory and Applications
inferredcites →https://doi.org/10.1126/science.1202617openalex-snapshot
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
inferredcites →https://doi.org/10.1126/science.1219364openalex-snapshot
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
inferredcites →https://doi.org/10.1146/annurev.bb.06.060177.001055openalex-snapshot
AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE
inferredcites →https://doi.org/10.1146/annurev.bb.19.060190.001505openalex-snapshot
Electrostatic Interactions in Macromolecules: Theory and Applications
inferredcites →https://doi.org/10.1186/1471-2105-10-407openalex-snapshot
Protein-protein docking using region-based 3D Zernike descriptors
inferredcites →https://doi.org/10.2174/138920311796957612openalex-snapshot
Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.48550/arxiv.1412.6980openalex-snapshot
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inferredcites →https://doi.org/10.48550/arxiv.1712.04621openalex-snapshot
The Effectiveness of Data Augmentation in Image Classification using Deep Learning
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Open3D: A Modern Library for 3D Data Processing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/prot.25993openalex-snapshot
A new method for protein characterization and classification using geometrical features for 3D face analysis: An example of tubulin structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00695openalex-snapshot
Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00687openalex-snapshot
GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
inferred← citeshttps://doi.org/10.1038/s42003-022-03445-2openalex-snapshot
PepNN: a deep attention model for the identification of peptide binding sites
inferred← citeshttps://doi.org/10.1101/2022.10.07.511322openalex-snapshot
EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
inferred← citeshttps://doi.org/10.1101/617860openalex-snapshot
Deep learning enables therapeutic antibody optimization in mammalian cells by deciphering high-dimensional protein sequence space
inferred← citeshttps://doi.org/10.1101/759498openalex-snapshot
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
inferred← citeshttps://doi.org/10.1109/iccvw.2019.00509openalex-snapshot
SpiralNet++: A Fast and Highly Efficient Mesh Convolution Operator
inferred← citeshttps://doi.org/10.1109/tcbbio.2025.3627203openalex-snapshot
Deep Learning-Driven Protein-Ligand Binding Affinity Prediction: Data, Architecture, Training and Evaluation
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010271openalex-snapshot
Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
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Presentation of Neutralizing Antibodies in Single- or Pooled-Convalescent Immune Plasma from Donors to Prevent the Current SARS-CoV-2 Pandemic
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A Review of Deep Learning Methods for Antibodies
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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
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