Jiye Shi

Publication Activity (10 Years)

Years Active: 2001-2022
Publications (10 Years): 13

Top Topics

Protein Structure Prediction

Prediction Accuracy

Top Venues

J. Chem. Inf. Model.

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Jiangbo Liu, Xinxin Jing, Mengmeng Liu, Fan Li, Min Li, Qian Li, Jiye Shi, Jiang Li, Lihua Wang, Xiuhai Mao, Xiaolei Zuo, Chunhai Fan
Mechano-fluorescence actuation in single synaptic vesicles with a DNA framework nanomachine. Sci. Robotics 7 (73) (2022)
Dominik Schwarz, Guy Georges, Sebastian Kelm, Jiye Shi, Anna Vangone, Charlotte M. Deane
Co-evolutionary distance predictions contain flexibility information. Bioinform. 38 (1) (2021)
Andreu Vall, Yogesh Sabnis, Jiye Shi, Reiner Class, Sepp Hochreiter, Günter Klambauer
The Promise of AI for DILI Prediction. Frontiers Artif. Intell. 4 (2021)
Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
Public Baseline and shared response structures support the theory of antibody repertoire functional commonality. PLoS Comput. Biol. 17 (3) (2021)
Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
TCRBuilder: multi-state T-cell receptor structure prediction. Bioinform. 36 (11) (2020)
Matthew I. J. Raybould, Claire Marks, Alan P. Lewis, Jiye Shi, Alexander Bujotzek, Bruck Taddese, Charlotte M. Deane
Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48 (Database-Issue) (2020)
Zhijian Xu, Qian Zhang, Jiye Shi, Weiliang Zhu
Underestimated Noncovalent Interactions in Protein Data Bank. J. Chem. Inf. Model. 59 (8) (2019)
Zhaoqiang Chen, Xinben Zhang, Cheng Peng, Jinan Wang, Zhijian Xu, Kaixian Chen, Jiye Shi, Weiliang Zhu
D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. J. Chem. Inf. Model. 59 (8) (2019)
Saulo Henrique Pires de Oliveira, Eleanor C. Law, Jiye Shi, Charlotte M. Deane
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. Bioinform. 34 (7) (2018)
Claire Marks, Jiye Shi, Charlotte M. Deane
Predicting loop conformational ensembles. Bioinform. 34 (6) (2018)
Qian Zhang, Zhijian Xu, Jiye Shi, Weiliang Zhu
Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. J. Chem. Inf. Model. 57 (7) (2017)
Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M. Deane
Comparing co-evolution methods and their application to template-free protein structure prediction. Bioinform. 33 (3) (2017)
Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M. Deane
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinform. 33 (9) (2017)
Nathaniel Powers, Alexander Alling, Kiara Osolinsky, Tolga Soyata, Meng Zhu, Haoliang Wang, He Ba, Wendi B. Heinzelman, Jiye Shi, Minseok Kwon
The Cloudlet Accelerator: Bringing Mobile-Cloud Face Recognition into Real-Time. GLOBECOM Workshops (2015)
James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design. PLoS Comput. Biol. 10 (9) (2014)
James Dunbar, Konrad Krawczyk, Jinwoo Leem, Terry Baker, Angelika Fuchs, Guy Georges, Jiye Shi, Charlotte M. Deane
SAbDab: the structural antibody database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Minseok Kwon, Zuochao Dou, Wendi B. Heinzelman, Tolga Soyata, He Ba, Jiye Shi
Use of Network Latency Profiling and Redundancy for Cloud Server Selection. IEEE CLOUD (2014)
Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane
Improving B-cell epitope prediction and its application to global antibody-antigen docking. Bioinform. 30 (16) (2014)
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp
Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J. Chem. Inf. Model. 54 (9) (2014)
Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Memoir: template-based structure prediction for membrane proteins. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
He Ba, Wendi Rabiner Heinzelman, Charles-Antoine Janssen, Jiye Shi
Mobile computing - A green computing resource. WCNC (2013)
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Environment specific substitution tables improve membrane protein alignment. Bioinform. 27 (13) (2011)
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
MEDELLER: homology-based coordinate generation for membrane proteins. Bioinform. 26 (22) (2010)
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
iMembrane: homology-based membrane-insertion of proteins. Bioinform. 25 (8) (2009)
A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini
DDBASE2.0: updated domain database with improved identification of structural domains. Bioinform. 19 (14) (2003)
Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinform. 17 (8) (2001)