D3CARP: a comprehensive platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening.

[BibT_eX]

[DOI]

Yulong Shi

Xinben Zhang

Comput. Biol. Medicine, September, 2023

Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, February, 2023

2022

Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

Conserved protein targets for developing pan-coronavirus drugs based on sequence and 3D structure similarity analyses.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, 2022

D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, 2022

D3PM: a comprehensive database for protein motions ranging from residue to domain.

[BibT_eX]

[DOI]

BMC Bioinform., 2022

D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

2021

D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2021

Ligand-based approach for predicting drug targets and for virtual screening against COVID-19.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

Highly Dynamic Bipedal Locomotion via an Improved Virtual Model Algorithm.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Robotics and Biomimetics, 2021

Design of BRAVER - a bipedal robot actuated via proprioceptive electric motor.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Robotics and Biomimetics, 2021

2020

High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Interaction Nature and Computational Methods for Halogen Bonding: A Perspective.

[BibT_eX]

[DOI]

Zhengdan Zhu

Zhijian Xu

Weiliang Zhu

J. Chem. Inf. Model., 2020

Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge.

[BibT_eX]

[DOI]

J. Comput. Chem., 2020

2019

Underestimated Noncovalent Interactions in Protein Data Bank.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2019

D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2019

2017

Combined Virtual Screening and Substructure Search for Discovery of Novel FABP4 Inhibitors.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., September, 2017

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., July, 2017

The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design.

[BibT_eX]

[DOI]

Qian Zhang

Zhijian Xu

Weiliang Zhu

J. Chem. Inf. Model., 2017

mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework.

[BibT_eX]

[DOI]

Proceedings of the 17th IEEE/ACM International Symposium on Cluster, 2017

2016

mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer.

[BibT_eX]

[DOI]

Proceedings of the 15th IEEE/ACM International Symposium on Cluster, 2015

mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors.

[BibT_eX]

[DOI]

Proceedings of the 15th IEEE/ACM International Symposium on Cluster, 2015

mD3DOCKxb: A Deep Parallel Optimized Software for Molecular Docking with Intel Xeon Phi Coprocessors.

[BibT_eX]

[DOI]

Proceedings of the 15th IEEE/ACM International Symposium on Cluster, 2015

2014

Algorithm and Its Implementation of Vehicle Safety Distance Control Based on the Numerical Simulation.

[BibT_eX]

[DOI]

Jingguo Qu

Yuhuan Cui

Weiliang Zhu

J. Networks, 2014

The Study and Improvement of Unidimensional Search about Nonlinear Optimization.

[BibT_eX]

[DOI]

Yuhuan Cui

Jingguo Qu

Weiliang Zhu

J. Networks, 2014

Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

Estimation of acute oral toxicity in rat using local lazy learning.

[BibT_eX]

[DOI]

J. Cheminformatics, 2014

<i>In silico</i> site of metabolism prediction for human UGT-catalyzed reactions.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against <i>Mycobacterium tuberculosis</i> by Virtual Screening and Bioassay.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2013

A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2013

2012

Estimation of Carcinogenicity Using Molecular Fragments Tree.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

2011

Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

2010

Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2010

2009

Site of metabolism prediction for six biotransformations mediated by cytochromes P450.

[BibT_eX]

[DOI]

Bioinform., 2009

2008

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2008

PDTD: a web-accessible protein database for drug target identification.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

2007

Why does beta-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies.

[BibT_eX]

[DOI]

Comput. Biol. Chem., 2007

2006

TarFisDock: a web server for identifying drug targets with docking approach.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2006

QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2006

Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4, 1-benzoxazepinone analogues.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2006

Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine.

[BibT_eX]