Jiye Shi

发表

Predicting loop conformational ensembles

Jiye Shi, Charlotte M. Deane, Claire Marks, 2018, Bioinform..

Comparing co-evolution methods and their application to template-free protein structure prediction

Jiye Shi, Charlotte M. Deane, Saulo Henrique Pires de Oliveira, 2016, Bioinform..

Fragment‐based modeling of membrane protein loops: Successes, failures, and prospects for the future

Sebastian Kelm, Jiye Shi, Anna Vangone, 2014, Proteins.

Mobile computing - A green computing resource

Jiye Shi, Wendi B. Heinzelman, He Ba, 2013, 2013 IEEE Wireless Communications and Networking Conference (WCNC).

Crowdsourcing Yields a New Standard for Kinks in Protein Helices

Jiye Shi, Charlotte M. Deane, Bernhard Knapp, 2014, J. Chem. Inf. Model..

DDBASE2.0: updated domain database with improved identification of structural domains

Jiye Shi, Ramanathan Sowdhamini, Tom L. Blundell, 2003, Bioinform..

Computational Exploration of Conformational Transitions in Protein Drug Targets.

Jiye Shi, Benjamin P. Cossins, Benjamin P Cossins, 2018, Methods in molecular biology.

Sphinx: merging knowledge‐based and ab initio approaches to improve protein loop prediction

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2017, Bioinform..

Camelid Single-Domain Antibodies Analysis and Modeling of the Variable Region of

Jiye Shi, Jeffrey J. Gray, Kayode Sanni, 2011 .

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

Jiye Shi, Alex Bateman, Kenji Mizuguchi, 2001, Bioinform..

Computational studies of protein helix kinks

Jiye Shi, 2014 .

Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation.

Jiye Shi, Weiliang Zhu, Qiang Shao, 2017, Journal of chemical theory and computation.

ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

Jiye Shi, Charlotte M. Deane, James Dunbar, 2016, mAbs.

Five computational developability guidelines for therapeutic antibody profiling

Jiye Shi, Claire Marks, Konrad Krawczyk, 2019, Proceedings of the National Academy of Sciences.

Improving B-cell epitope prediction and its application to global antibody-antigen docking

Jiye Shi, Charlotte M. Deane, Konrad Krawczyk, 2014, Bioinform..

Solving mazes with single-molecule DNA navigators

Jie Chao, Wei Huang, Jiye Shi, 2018, Nature Materials.

Volunteer Computing on Mobile Devices: State of the Art and Future Research Directions

Wendi Heinzelman, Jiye Shi, Cristiano Tapparello, 2016 .

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries

Jiye Shi, Mark S. P. Sansom, Zara A. Sands, 2015, Journal of chemical theory and computation.

Accelerating Mobile-Cloud Computing: A Survey

Wendi Heinzelman, Jiye Shi, Minseok Kwon, 2014 .

SAbDab: the structural antibody database

Jiye Shi, Charlotte M. Deane, Konrad Krawczyk, 2013, Nucleic Acids Res..

Memoir: template-based structure prediction for membrane proteins

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2013, Nucleic Acids Res..

Implementing digital computing with DNA-based switching circuits

Jiye Shi, Fei Wang, Chunhai Fan, 2020, Nature Communications.

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design

Jiye Shi, Charlotte M. Deane, Bernhard Knapp, 2014, PLoS Comput. Biol..

Environment specific substitution tables improve membrane protein alignment

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2011, Bioinform..

Efficient Sampling for the Prediction of Long and Multidomain Protein Structures

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2018 .

The Cloudlet Accelerator: Bringing Mobile-Cloud Face Recognition into Real-Time

Jiye Shi, Wendi B. Heinzelman, Meng Zhu, 2015, 2015 IEEE Globecom Workshops (GC Wkshps).

Use of Network Latency Profiling and Redundancy for Cloud Server Selection

Jiye Shi, Wendi B. Heinzelman, Minseok Kwon, 2014, 2014 IEEE 7th International Conference on Cloud Computing.

The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines

Jiye Shi, Claire Marks, Matthew I. J. Raybould, 2018, bioRxiv.

MEDELLER: homology-based coordinate generation for membrane proteins

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2010, Bioinform..

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction

Jiye Shi, Charlotte M. Deane, Saulo Henrique Pires de Oliveira, 2018, Bioinform..

Co-evolutionary distance predictions contain flexibility information

Sebastian Kelm, Jiye Shi, Charlotte M. Deane, 2021, Bioinform..

Investigating the potential for a limited quantum speedup on protein lattice problems

Jiye Shi, Garrett M Morris, Simon C Benjamin, 2020, New Journal of Physics.

The Promise of AI for DILI Prediction

Jiye Shi, Sepp Hochreiter, Günter Klambauer, 2021, Frontiers in Artificial Intelligence.

Public Baseline and shared response structures support the theory of antibody repertoire functional commonality

Jiye Shi, Charlotte M. Deane, Claire Marks, 2021, PLoS Comput. Biol..

Smart Drug Delivery Nanocarriers with Self‐Assembled DNA Nanostructures

Jiye Shi, Chunhai Fan, Qing Huang, 2013 .

Hydrogen Sulfide-Activatable Second Near-Infrared Fluorescent Nanoassemblies for Targeted Photothermal Cancer Therapy.

Jiye Shi, Wei Gao, Chunhai Fan, 2018, Nano letters.

Antibody side chain conformations are position‐dependent

Jiye Shi, Jinwoo Leem, Guy Georges, 2018, Proteins.

Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction

Jiye Shi, Chunhai Fan, Qian Li, 2020, Nature Protocols.

Building a Better Fragment Library for De Novo Protein Structure Prediction

Jiye Shi, Charlotte M. Deane, Saulo H. P. de Oliveira, 2015, PloS one.

Hybridization chain reaction amplification of microRNA detection with a tetrahedral DNA nanostructure-based electrochemical biosensor.

Jiye Shi, Chunhai Fan, Ping Wang, 2014, Analytical chemistry.

DNA Hydrogel with Aptamer-Toehold-Based Recognition, Cloaking, and Decloaking of Circulating Tumor Cells for Live Cell Analysis.

Jie Chao, Jiye Shi, Wei Huang, 2017, Nano letters.

Examining the Conservation of Kinks in Alpha Helices

Sebastian Kelm, Jiye Shi, Charlotte M Deane, 2016, PloS one.

In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time.

Jiye Shi, Chunhai Fan, Ratnesh Lal, 2018, Angewandte Chemie.

Preservation of DNA Nanostructure Carriers: Effects of Freeze-Thawing and Ionic Strength during Lyophilization and Storage.

Jiye Shi, Li Li, Lihua Wang, 2017, ACS applied materials & interfaces.

Programmable engineering of a biosensing interface with tetrahedral DNA nanostructures for ultrasensitive DNA detection.

Jiye Shi, Chunhai Fan, Xiaolei Zuo, 2015, Angewandte Chemie.

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2014, The journal of physical chemistry. B.

Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2019, ACS omega.

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

Jiye Shi, Weiliang Zhu, Qiang Shao, 2012, The Journal of chemical physics.

DNA-Origami-Based Assembly of Anisotropic Plasmonic Gold Nanostructures.

Jie Chao, Jiye Shi, Chunhai Fan, 2017, Small.

Thera-SAbDab: the Therapeutic Structural Antibody Database

Jiye Shi, Charlotte M. Deane, Claire Marks, 2020, Nucleic Acids Res..

An Intelligent DNA Nanorobot with in Vitro Enhanced Protein Lysosomal Degradation of HER2.

Jiye Shi, Chunhai Fan, Qian Li, 2019, Nano letters.

Catalysis-Driven Self-Thermophoresis of Janus Plasmonic Nanomotors.

Jiye Shi, Chunhai Fan, Fei Wang, 2017, Angewandte Chemie.

DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury

Jiye Shi, Hao Yan, Peng Huang, 2018, Nature Biomedical Engineering.

Thermodynamics calculation of protein–ligand interactions by QM/MM polarizable charge parameters

Jiye Shi, Weiliang Zhu, Benjamin P. Cossins, 2016, Journal of biomolecular structure & dynamics.

An Exonuclease III-Powered, On-Particle Stochastic DNA Walker.

Jie Chao, Wei Huang, Jiye Shi, 2017, Angewandte Chemie.

Mapping central α-helix linker mediated conformational transition pathway of calmodulin via simple computational approach.

Jiye Shi, Xiangke Liao, Weiliang Zhu, 2014, The journal of physical chemistry. B.

Stability and Characteristics of the Halogen Bonding Interaction in an Anion-Anion Complex: A Computational Chemistry Study.

Jiye Shi, Yang Yang, Zhijian Xu, 2016, The journal of physical chemistry. B.

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density

Sebastian Kelm, Jiye Shi, Charlotte M Deane, 2017, Nature Communications.

Multiple-Armed Tetrahedral DNA Nanostructures for Tumor-Targeting, Dual-Modality in Vivo Imaging.

Jiye Shi, Chunhai Fan, Qian Li, 2016, ACS applied materials & interfaces.

Evolutionary Trace analysis of TGF-β and related growth factors

Jiye Shi, Tom L. Blundell, C. A. Innis, 2000 .

Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions.

Jiye Shi, Chunhai Fan, Shiping Song, 2017, Journal of the American Chemical Society.

Gold-nanoparticle-mediated jigsaw-puzzle-like assembly of supersized plasmonic DNA origami.

Jie Chao, Wei Huang, Jiye Shi, 2015, Angewandte Chemie.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

Sebastian Kelm, Jiye Shi, Claire Marks, 2017, Bioinformatics.

Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

Jiye Shi, Richard D. Taylor, Terry Baker, 2017, Scientific Reports.

Smart Drug Delivery Nanocarriers with Self‐Assembled DNA Nanostructures

Jiye Shi, Chunhai Fan, Qing Huang, 2013, Advanced materials.

Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells.

Jiye Shi, Chunhai Fan, Qian Li, 2014, Angewandte Chemie.

Force fields and scoring functions for carbohydrate simulation.

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2015, Carbohydrate research.

Multicolor Gold-Silver Nano-Mushrooms as Ready-to-Use SERS Probes for Ultrasensitive and Multiplex DNA/miRNA Detection.

Jiye Shi, Sanjay Mathur, Chunhai Fan, 2017, Analytical chemistry.

Portable detection of clenbuterol using a smartphone-based electrochemical biosensor with electric field-driven acceleration

Jiye Shi, Chunhai Fan, Yanzhi Dou, 2016 .

Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design?

Jiye Shi, Yang Yang, Shujin Li, 2015, The journal of physical chemistry. B.

The H3 loop of antibodies shows unique structural characteristics

Jiye Shi, Cristian Regep, Guy Georges, 2017, Proteins.

Real-time visualization of clustering and intracellular transport of gold nanoparticles by correlative imaging

Jiye Shi, Chunhai Fan, Qian Li, 2017, Nature Communications.

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2015, Journal of Molecular Modeling.

Transfer of Two-Dimensional Oligonucleotide Patterns onto Stereocontrolled Plasmonic Nanostructures through DNA-Origami-Based Nanoimprinting Lithography.

Jie Chao, Wei Huang, Jiye Shi, 2016, Angewandte Chemie.

Constructing Higher-Order DNA Nanoarchitectures with Highly Purified DNA Nanocages.

Jiye Shi, Chunhai Fan, Qian Li, 2015, ACS applied materials & interfaces.

Graphene Oxide‐Based Antibacterial Cotton Fabrics

Jiye Shi, Chunhai Fan, Qing Huang, 2013, Advanced healthcare materials.

Biodistribution and pulmonary toxicity of intratracheally instilled graphene oxide in mice

Jiye Shi, Yi Zhang, Bo Li, 2013 .