{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/geometric-transformers-for-protein-interface","title":"Geometric Transformers for Protein Interface Contact Prediction","arxiv_id":"2110.02423","date":"2021-10-06","proceeding":"ICLR 2022 4","authors":["Alex Morehead","Chen Chen","Jianlin Cheng"],"abstract":"Computational methods for predicting the interface contacts between proteins come highly sought after for drug discovery as they can significantly advance the accuracy of alternative approaches, such as protein-protein docking, protein function analysis tools, and other computational methods for protein bioinformatics. In this work, we present the Geometric Transformer, a novel geometry-evolving graph transformer for rotation and translation-invariant protein interface contact prediction, packaged within DeepInteract, an end-to-end prediction pipeline. DeepInteract predicts partner-specific protein interface contacts (i.e., inter-protein residue-residue contacts) given the 3D tertiary structures of two proteins as input. In rigorous benchmarks, DeepInteract, on challenging protein complex targets from the 13th and 14th CASP-CAPRI experiments as well as Docking Benchmark 5, achieves 14% and 1.1% top L/5 precision (L: length of a protein unit in a complex), respectively. In doing so, DeepInteract, with the Geometric Transformer as its graph-based backbone, outperforms existing methods for interface contact prediction in addition to other graph-based neural network backbones compatible with DeepInteract, thereby validating the effectiveness of the Geometric Transformer for learning rich relational-geometric features for downstream tasks on 3D protein structures.","url_abs":"https://arxiv.org/abs/2110.02423v5","url_pdf":"https://arxiv.org/pdf/2110.02423v5.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"geometric-transformers-for-protein-interface","repo_url":"https://github.com/bioinfomachinelearning/deepinteract","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}},{"paper_slug":"geometric-transformers-for-protein-interface","repo_url":"https://github.com/BioinfoMachineLearning/DeepRefine","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"prediction","task_name":"Prediction"},{"task_slug":"translation","task_name":"Translation"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"graph-transformer","method_name":"Graph Transformer"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"lapeigen","method_name":"LapEigen"},{"method_slug":"laplacian-pe","method_name":"Laplacian PE"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2110.02423","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}