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YiWu Sun

dblp:335/1629 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › machine learning for biology
multimodal protein representation
0.712023
Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization · NeurIPS 2023
Bioinformatics and computational biology › protein structure prediction
protein-protein docking
0.712023
Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization · NeurIPS 2023
Bioinformatics and computational biology
protein structure prediction
0.712023
Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization · NeurIPS 2023
Bioinformatics and computational biology › protein structure prediction › protein-protein docking
rigid-body docking
0.712023
Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization · NeurIPS 2023

Methods — techniques the papers use, named apart from their topics

spectral estimation · 0.7gradient unrolling · 0.7cross-modal transformer · 0.7bi-level optimization · 0.7
YearPublicationVenuePosition
2023 Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization
abstract
The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies. Rigid protein docking, a fundamental problem in this field, aims to predict the 3D structure of complexes from their unbound states without conformational changes. In this scenario, we have access to two types of valuable information: sequence-modal information, such as coevolutionary data obtained from multiple sequence alignments, and structure-modal information, including the 3D conformations of rigid structures. However, existing docking methods typically utilize single-modal information, resulting in suboptimal predictions. In this paper, we propose xTrimoBiDock (or BiDock for short), a novel rigid docking model that effectively integrates sequence- and structure-modal information through bi-level optimization. Specifically, a cross-modal transformer combines multimodal information to predict an inter-protein distance map. To achieve rigid docking, the roto-translation transformation is optimized to align the docked pose with the predicted distance map. In order to tackle this bi-level optimization problem, we unroll the gradient descent of the inner loop and further derive a better initialization for roto-translation transformation based on spectral estimation. Compared to baselines, BiDock achieves a promising result of a maximum 234% relative improvement in challenging antibody-antigen docking problem.
YiWu Sun, Shaochuan Li, Cheng Yang 0002, Xingyi Cheng, Chuan Shi 0001
NeurIPS2