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List of works by Jiye Shi

A Multi-Crystal Method for Extracting Obscured Signal from Crystallographic Electron Density

article published in 2016

A bubble-mediated intelligent microscale electrochemical device for single-step quantitative bioassays

scientific article published on 14 April 2014

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

scientific article (publication date: 24 April 2017)

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

scientific article published on 10 May 2015

ABangle: characterising the VH-VL orientation in antibodies

scientific article published on 24 May 2013

Accelerating Mobile-Cloud Computing

scholarly article

Analysis and modeling of the variable region of camelid single-domain antibodies

scientific article

Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking

scientific article published on 4 September 2013

Characterization of the interaction of sclerostin with the low density lipoprotein receptor-related protein (LRP) family of Wnt co-receptors.

scientific article

Combining modelling and mutagenesis studies of synaptic vesicle protein 2A to identify a series of residues involved in racetam binding

scientific article published in October 2011

Conjugation of dexamethasone to C60 for the design of an anti-inflammatory nanomedicine with reduced cellular apoptosis

scientific article published on 17 May 2013

Constructing Higher-Order DNA Nanoarchitectures with Highly Purified DNA Nanocages

Cotranscriptionally Folded RNA Nanostructures Pave the Way to Intracellular Nanofabrication

scientific article published in 2014

Crowdsourcing yields a new standard for kinks in protein helices.

scientific article published on 3 September 2014

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

scientific article

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

scientific article published on 3 August 2017

DNA origami cryptography for secure communication

scientific article published on 29 November 2019

DNA-directed assembly of gold nanohalo for quantitative plasmonic imaging of single-particle catalysis

scientific article published on 30 March 2015

Discovery of N-substituted 3-arylisoquinolone derivatives as antitumor agents originating from O-substituted 3-arylisoquinolines via [2,3] or [3,3] rearrangement.

scientific article published on 6 March 2014

Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir.

scientific article published on 27 May 2015

Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform.

scientific article published on 16 June 2016

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

scientific article published in September 2012

Environment specific substitution tables improve membrane protein alignment ⬇️

scientific article published on July 2011

Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis.

scientific article published on December 2000

Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design

scientific article

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

scientific article

Five computational developability guidelines for therapeutic antibody profiling

scientific article published on 14 February 2019

Force fields and scoring functions for carbohydrate simulation.

scientific article published on 8 November 2014

Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future

scientific article

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

scientific article

Graphene oxide-based antibacterial cotton fabrics.

scientific article published on 11 March 2013

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

scientific article published in August 2001

Helix kinks are equally prevalent in soluble and membrane proteins.

scientific article

High Resolution NMR-based Model for the Structure of a scFv-IL-1  Complex: POTENTIAL FOR NMR AS A KEY TOOL IN THERAPEUTIC ANTIBODY DESIGN AND DEVELOPMENT

scientific article

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

scientific article published on 4 February 2014

Implementing digital computing with DNA-based switching circuits

scientific article published on 08 January 2020

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

scientific article published on 21 April 2014

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

scientific article

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

scientific article published on 19 August 2015

MEDELLER: homology-based coordinate generation for membrane proteins ⬇️

scientific article published on October 5, 2010

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

scientific article published on 05 August 2014

Memoir: template-based structure prediction for membrane proteins

scientific article

Mobile computing - A green computing resource

Molecular dynamics simulation indicating cold denaturation of β-hairpins

scientific article

Multi-algorithm and multi-model based drug target prediction and web server

scientific article

Nanoplasmonic imaging of latent fingerprints with explosive RDX residues

scientific article published on 20 August 2015

Nanoscale optical probes for cellular imaging

scientific article published on 06 January 2014

Pattern recognition analysis of proteins using DNA-decorated catalytic gold nanoparticles

scientific article published on 27 February 2013

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

scientific article

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

scientific article published on 17 July 2017

Programming bulk enzyme heterojunctions for biosensor development with tetrahedral DNA framework

scientific article published on 11 February 2020

Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization

scientific article published on 01 March 2019

Real time in vitro regulation of DNA methylation using a 5-fluorouracil conjugated DNA-based stimuli-responsive platform

scientific article published on 25 March 2013

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

scientific article

Recent progress in natural products as DPP-4 inhibitors.

scientific article published on June 2015

SAbDab: the structural antibody database

scientific article

Scaffolded biosensors with designed DNA nanostructures

Self-assembly of poly-adenine-tailed CpG oligonucleotide-gold nanoparticle nanoconjugates with immunostimulatory activity

scientific article published on 21 August 2013

Separation and peroxisome proliferator-activated receptor-γ agonist activity evaluation of synthetic racemic bavachinin enantiomers

scientific article

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

scientific article

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

scientific article published on 14 May 2014

Size-dependent programming of the dynamic range of graphene oxide-DNA interaction-based ion sensors

scientific article published on 26 March 2014

Smart drug delivery nanocarriers with self-assembled DNA nanostructures

scientific article published on 13 June 2013

The universality of β-hairpin misfolding indicated by molecular dynamics simulations

scientific article published in October 2013

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

scientific article

Unraveling the Role of Hydrogen Peroxide in α-Synuclein Aggregation Using an Ultrasensitive Nanoplasmonic Probe

scientific article published on 23 January 2015

Unstable, metastable, or stable halogen bonding interaction involving negatively charged donors? A statistical and computational chemistry study

scientific article published on 25 November 2014

Valency-Controlled Framework Nucleic Acid Signal Amplifiers

scientific article published on 19 April 2018

iMembrane: homology-based membrane-insertion of proteins.

scientific article

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