闫成飞｜华中科技大学｜学者主页

期刊论文

2026

ChengfeiYan/PLMDA-PPI: PLMDA-PPI

Chengfei Yan

Zenodo (CERN European Organization for Nuclear Research)

DOI

2026

A geometry-over-coevolution principle governs protein complex assembly in AlphaFold

Shuang Li, Z. Mu, Chengfei Yan

bioRxiv

DOI

2025

Mechanism-Aware Inductive Bias Enhances Generalization in Protein-Protein Interaction Prediction

Shu-Chen Deng, Xu Wan, Z. Mu, Sheng-Qiang Huang, Chengfei Yan

bioRxiv

DOI

2024

Author Response: Protein language model-embedded geometric graphs power inter-protein contact prediction

Yunda Si, Chengfei Yan

DOI

2023

Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models

Yunda Si, Chengfei Yan

Briefings in Bioinformatics

DOI

2021

Protein Complex Structure Prediction Powered by Multiple Sequence Alignments of Interologs from Multiple Taxonomic Ranks and AlphaFold2

Yunda Si, Chengfei Yan

bioRxiv

DOI

2021

Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function

Yunda Si, Chengfei Yan

bioRxiv

DOI

2018

MDockPeP: An ab-initio protein-peptide docking server

Xian-Jin Xu, Chengfei Yan, Xiaoqin Zou

Journal of Computational Chemistry

DOI

2018

Blind Prediction of Protein-Peptide Complex Structures: A Novel Method and a Web Server

Xian-Jin Xu, Chengfei Yan, Xiaoqin Zou

DOI

2017

The Usage of ACCLUSTER for Peptide Binding Site Prediction.

Chengfei Yan, Xian-Jin Xu, Xiaoqin Zou

Methods in molecular biology

DOI

2017

Modeling Protein Flexibility in Molecular Docking

Chengfei Yan, Xiaoqin Zou

DOI

2017

Improving Binding Mode and Binding Affinity Predictions of Docking by Ligand-based Search of Protein Conformations: Evaluation in D3R Grand Challenge 2015

Xian-Jin Xu, Chengfei Yan, Xiaoqin Zou

Journal of Computer-Aided Molecular Design

DOI

2016

Performance of MDockPP in CAPRI Rounds 28–29 and 31–35 including the prediction of water-mediated interactions

Xian-Jin Xu, Liming Qiu, Chengfei Yan, Zhiwei Ma, S. Grinter, Xiaoqin Zou

Proteins: Structure, Function, and Bioinformatics

DOI

2016

Predicting protein-peptide interactions from scratch

Chengfei Yan, Xian-Jin Xu, Xiaoqin Zou

2016

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

Chengfei Yan, Xian-Jin Xu, Xiaoqin Zou

Structure

DOI

2016

Developing molecular docking methods to model protein interactions

Chengfei Yan

2016

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

M. Lensink, S. Velankar, A. Kryshtafovych, Shengua Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernández-Fuentes, Shruthi Viswanath, R. Elber, Sergei Grudinin, P. Popov, Émilie Neveu, Hasup Lee, M. Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, Raphael A. G. Chaleil, P. Bates, E. Ben-Zeev, M. Eisenstein, S. Negi, Z. Weng, T. Vreven, B. Pierce, Tyler Borrman, Jinchao Yu, F. Ochsenbein, R. Guérois, A. Vangone, J. Rodrigues, G. V. van Zundert, M. Nellen, Li C. Xue, E. Karaca, A. Melquiond, K. Visscher, P. Kastritis, A. Bonvin, Xian-Jin Xu, Liming Qiu, Chengfei Yan, Ji-Long Li, Zhiwei Ma, Jian-Lin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyungrae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodríguez, D. Kihara, Xiao-Feng Yu, Neil J. Bruce, Jonathan C. Fuller, R. Wade, I. Anishchenko, P. Kundrotas, I. Vakser, K. Imai, K. Yamada, Toshiyuki Oda, Tsukasa Nakamura, K. Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, I. Moal, J. Fernández-Recio, Jong Young Joung, Jong Yun Kim, K. Joo, Jooyoung Lee, D. Kozakov, S. Vajda, Scott E. Mottarella, D. Hall, Dmitri Beglov, A. Mamonov, B. Xia, T. Bohnuud, C. D. Del Carpio, Eichiro Ichiishi, Nicholas A. Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S. Wodak

Proteins: Structure, Function, and Bioinformatics

DOI

2015

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

Chengfei Yan, Xiaoqin Zou

Journal of Computational Chemistry

DOI

2015

Iterative Knowledge-based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

Chengfei Yan, S. Grinter, B. Merideth, Zhiwei Ma, Xiaoqin Zou

Journal of Chemical Information and Modeling

DOI

2015

MDock: An Ensemble Docking Suite for Molecular Docking, Scoring and In Silico Screening

Chengfei Yan, Xiaoqin Zou

DOI

2013

Automated large-scale file preparation, docking, and scoring: Evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource Benchmark

S. Grinter, Chengfei Yan, Sheng-You Huang, Lin Jiang, Xiaoqin Zou

Journal of Chemical Information and Modeling

DOI

2013

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI

Sheng-You Huang, Chengfei Yan, S. Grinter, Shan Chang, Lin Jiang, Xiaoqin Zou

Proteins: Structure, Function, and Bioinformatics

DOI

预印本

2025

Mechanism-Aware Protein-Protein Interaction Prediction via Contact-Guided Dual Attention on Protein Language Models

Chengfei Yan, Shuchen Deng, Xuanjun Wan, Zichun Mu, Sheng‐You Huang

Research Square

DOI

精选作品

期刊论文

ChengfeiYan/PLMDA-PPI: PLMDA-PPI

A geometry-over-coevolution principle governs protein complex assembly in AlphaFold

Mechanism-Aware Inductive Bias Enhances Generalization in Protein-Protein Interaction Prediction

Author Response: Protein language model-embedded geometric graphs power inter-protein contact prediction

Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models

Protein Complex Structure Prediction Powered by Multiple Sequence Alignments of Interologs from Multiple Taxonomic Ranks and AlphaFold2

Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function

MDockPeP: An ab-initio protein-peptide docking server

Blind Prediction of Protein-Peptide Complex Structures: A Novel Method and a Web Server

The Usage of ACCLUSTER for Peptide Binding Site Prediction.

Modeling Protein Flexibility in Molecular Docking

Improving Binding Mode and Binding Affinity Predictions of Docking by Ligand-based Search of Protein Conformations: Evaluation in D3R Grand Challenge 2015

Performance of MDockPP in CAPRI Rounds 28–29 and 31–35 including the prediction of water-mediated interactions

Predicting protein-peptide interactions from scratch

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

Developing molecular docking methods to model protein interactions

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

Iterative Knowledge-based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

MDock: An Ensemble Docking Suite for Molecular Docking, Scoring and In Silico Screening

Automated large-scale file preparation, docking, and scoring: Evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource Benchmark

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI

预印本

Mechanism-Aware Protein-Protein Interaction Prediction via Contact-Guided Dual Attention on Protein Language Models