Works by Qi, Yifei

Results: 41

Efficient 1054 nm Raman Random Fiber Laser.

Published in:

Photonics, 2023, v. 10, n. 7, p. 851, doi. 10.3390/photonics10070851

By:

Wang, Pan;
Lin, Shengtao;
Zhang, Jiaojiao;
Bao, Xingyu;
Ni, Longqun;
Qi, Yifei;
Wang, Zinan

Publication type:

Article

HobPre: accurate prediction of human oral bioavailability for small molecules.

Published in:

Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-021-00580-6

By:

Wei, Min;
Zhang, Xudong;
Pan, Xiaolin;
Wang, Bo;
Ji, Changge;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

A sequence‐based model for identifying proteins undergoing liquid–liquid phase separation/forming fibril aggregates via machine learning.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 3, p. 1, doi. 10.1002/pro.4927

By:

Liao, Shaofeng;
Zhang, Yujun;
Han, Xinchen;
Wang, Tinglan;
Wang, Xi;
Yan, Qinglin;
Li, Qian;
Qi, Yifei;
Zhang, Zhuqing

Publication type:

Article

Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain.

Published in:

Toxins, 2017, v. 9, n. 10, p. 298, doi. 10.3390/toxins9100298

By:

Machen, Alexandra J.;
Akkaladevi, Narahari;
Trecazzi, Caleb;
O'Neil, Pierce T.;
Mukherjee, Srayanta;
Qi, Yifei;
Dillard, Rebecca;
Wonpil Im;
Gogol, Edward P.;
White, Tommi A.;
Fisher, Mark T.

Publication type:

Article

Discovery of novel inhibitors of SARS-CoV-2 main protease.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 23, p. 12526, doi. 10.1080/07391102.2021.1972041

By:

Zheng, Lei;
Chen, Yanmei;
Bao, Jingxiao;
He, Liping;
Dong, Suzhen;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 22, p. 12277, doi. 10.1080/07391102.2021.1971558

By:

Xia, Wei;
He, Liping;
Bao, Jingxiao;
Qi, Yifei;
Zhang, John Z.H.

Publication type:

Article

Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation.

Published in:

Chemical Biology & Drug Design, 2022, v. 99, n. 5, p. 662, doi. 10.1111/cbdd.14027

By:

Zheng, Lei;
Yang, Yunpeng;
Bao, Jingxiao;
He, Liping;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Analysis of the binding modes of the first‐ and second‐generation antiandrogens with respect to F876L mutation.

Published in:

Chemical Biology & Drug Design, 2021, v. 98, n. 1, p. 60, doi. 10.1111/cbdd.13848

By:

Shao, Guangfeng;
Bao, Jingxiao;
Pan, Xiaolin;
He, Xiao;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Identification of three new compounds that directly target human serine hydroxymethyltransferase 2.

Published in:

Chemical Biology & Drug Design, 2021, v. 97, n. 2, p. 221, doi. 10.1111/cbdd.13774

By:

Han, Yanfang;
He, Liping;
Qi, Yifei;
Zhao, Yue;
Pan, Yue;
Fang, Bohuan;
Li, Sha;
Zhang, John Z. H.;
Zhang, Lujia

Publication type:

Article

Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2.

Published in:

ChemPhysChem, 2020, v. 21, n. 3, p. 263, doi. 10.1002/cphc.201900903

By:

Huang, Dading;
Tian, Shuaizhen;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

Published in:

Scientific Reports, 2015, p. 8926, doi. 10.1038/srep08926

By:

Lee, Hui Sun;
Qi, Yifei;
Im, Wonpil

Publication type:

Article

Membrane associated collagen XIII promotes cancer metastasis and enhances anoikis resistance.

Published in:

2018

By:

Zhang, Hui;
Fredericks, Tricia;
Xiong, Gaofeng;
Qi, Yifei;
Rychahou, Piotr G.;
Li, Jia-Da;
Pihlajaniemi, Taina;
Xu, Wei;
Xu, Ren

Publication type:

journal article

SeBPPI: A Sequence-Based Protein–Protein Binding Predictor.

Published in:

Journal of Computational Biophysics & Chemistry, 2022, v. 21, n. 6, p. 729, doi. 10.1142/S2737416522500314

By:

Wang, Bo;
Mao, Jun;
Wei, Min;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Spectral Manipulations of Random Fiber Lasers: Principles, Characteristics, and Applications.

Published in:

Laser & Photonics Reviews, 2024, v. 18, n. 7, p. 1, doi. 10.1002/lpor.202400122

By:

Han, Bing;
Cheng, Qian;
Tao, Yiming;
Ma, Yuxi;
Liang, Houkun;
Ma, Rui;
Qi, Yifei;
Zhao, Yong;
Wang, Zinan;
Wu, Han

Publication type:

Article

CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations.

Published in:

Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 415, doi. 10.1002/jcc.26032

By:

Qi, Yifei;
Lee, Jumin;
Cheng, Xi;
Shen, Rong;
Islam, Shahidul M.;
Roux, Benoît;
Im, Wonpil

Publication type:

Article

Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 9, p. 1045, doi. 10.1002/jcc.25592

By:

Huang, Dading;
Qi, Yifei;
Song, Jianing;
Zhang, John Z. H.

Publication type:

Article

CHARMM‐GUI Nanodisc Builder for modeling and simulation of various nanodisc systems.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 7, p. 893, doi. 10.1002/jcc.25773

By:

Qi, Yifei;
Lee, Jumin;
Klauda, Jeffery B.;
Im, Wonpil

Publication type:

Article

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 27, p. 2354, doi. 10.1002/jcc.24895

By:

Hsu, Pin‐Chia;
Bruininks, Bart M. H.;
Jefferies, Damien;
Cesar Telles de Souza, Paulo;
Lee, Jumin;
Patel, Dhilon S.;
Marrink, Siewert J.;
Qi, Yifei;
Khalid, Syma;
Im, Wonpil

Publication type:

Article

CHARMM-GUI 10 years for biomolecular modeling and simulation.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1114, doi. 10.1002/jcc.24660

By:

Jo, Sunhwan;
Cheng, Xi;
Lee, Jumin;
Kim, Seonghoon;
Park, Sang‐Jun;
Patel, Dhilon S.;
Beaven, Andrew H.;
Lee, Kyu Il;
Rui, Huan;
Park, Soohyung;
Lee, Hui Sun;
Roux, Benoît;
MacKerell, Alexander D.;
Klauda, Jeffrey B.;
Qi, Yifei;
Im, Wonpil

Publication type:

Article

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.

Published in:

Journal of Computational Chemistry, 2014, v. 35, n. 27, p. 1997, doi. 10.1002/jcc.23702

By:

Wu, Emilia L.;
Cheng, Xi;
Jo, Sunhwan;
Rui, Huan;
Song, Kevin C.;
Dávila‐Contreras, Eder M.;
Qi, Yifei;
Lee, Jumin;
Monje‐Galvan, Viviana;
Venable, Richard M.;
Klauda, Jeffery B.;
Im, Wonpil

Publication type:

Article

ST-analyzer: A web-based user interface for simulation trajectory analysis.

Published in:

Journal of Computational Chemistry, 2014, v. 35, n. 12, p. 957, doi. 10.1002/jcc.23584

By:

Jeong, Jong Cheol;
Jo, Sunhwan;
Wu, Emilia L.;
Qi, Yifei;
Monje‐Galvan, Viviana;
Yeom, Min Sun;
Gorenstein, Lev;
Chen, Feng;
Klauda, Jeffery B.;
Im, Wonpil

Publication type:

Article

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro.

Published in:

Nucleic Acids Research, 2020, v. 48, n. D1, p. D320, doi. 10.1093/nar/gkz778

By:

Li, Qian;
Peng, Xiaojun;
Li, Yuanqing;
Tang, Wenqin;
Zhu, Jia'an;
Huang, Jing;
Qi, Yifei;
Zhang, Zhuqing

Publication type:

Article

Common ground on immune infiltration landscape and diagnostic biomarkers in diabetes-complicated atherosclerosis: an integrated bioinformatics analysis.

Published in:

Frontiers in Endocrinology, 2024, p. 01, doi. 10.3389/fendo.2024.1381229

By:

Yifei Qi;
Yan Zhang;
Shuang Guan;
Li Liu;
Hongqin Wang;
Yao Chen;
Qingbing Zhou;
Fengqin Xu;
Ying Zhang

Publication type:

Article

Common ground on immune infiltration landscape and diagnostic biomarkers in diabetes-complicated atherosclerosis: an integrated bioinformatics analysis.

Published in:

Frontiers in Endocrinology, 2024, p. 1, doi. 10.3389/fendo.2024.1381229

By:

Yifei Qi;
Yan Zhang;
Shuang Guan;
Li Liu;
Hongqin Wang;
Yao Chen;
Qingbing Zhou;
Fengqin Xu;
Ying Zhang

Publication type:

Article

Effects and mechanisms of Zhizi Chuanxiong herb pair against atherosclerosis: an integration of network pharmacology, molecular docking, and experimental validation.

Published in:

Chinese Medicine, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s13020-023-00874-x

By:

Zhang, Yan;
Qi, Yifei;
Jia, Zijun;
Li, Yiming;
Wu, Liqi;
Zhou, Qingbing;
Xu, Fengqin

Publication type:

Article

Dose-Dependent Variation of Synchronous Metabolites and Modules in a Yin/Yang Transformation Model of Appointed Ischemia Metabolic Networks.

Published in:

Frontiers in Neuroscience, 2021, v. 15, p. N.PAG, doi. 10.3389/fnins.2021.645185

By:

Qi, Yifei;
Zhou, Niwen;
Jiang, Qing;
Wang, Zhi;
Zhang, Yingying;
Li, Bing;
Xu, Wenjuan;
Liu, Jun;
Wang, Zhong;
Zhu, Lixing

Publication type:

Article

QoE Model Based Optimization for Streaming Media Service Considering Equipment and Environment Factors.

Published in:

Wireless Personal Communications, 2012, v. 66, n. 3, p. 595, doi. 10.1007/s11277-012-0739-7

By:

Han, Bingjun;
Zhang, Xin;
Qi, Yifei;
Gao, Yuehong;
Yang, Dacheng

Publication type:

Article

Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity.

Published in:

Scientific Reports, 2016, p. 20918, doi. 10.1038/srep20918

By:

Li, Chunmei;
Teng, Xin;
Qi, Yifei;
Tang, Bo;
Shi, Hailing;
Ma, Xiaomin;
Lai, Luhua

Publication type:

Article

Discovery of Novel Allosteric Effectors Based on the Predicted Allosteric Sites for <i>Escherichia coli</i> D-3-Phosphoglycerate Dehydrogenase.

Published in:

PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0094829

By:

Wang, Qian;
Qi, Yifei;
Yin, Ning;
Lai, Luhua

Publication type:

Article

Allosteric sites can be identified based on the residue-residue interaction energy difference.

Published in:

Proteins, 2015, v. 83, n. 8, p. 1375, doi. 10.1002/prot.24681

By:

Ma, Xiaomin;
Qi, Yifei;
Lai, Luhua

Publication type:

Article

Replica symmetry breaking in 1D Rayleigh scattering system: theory and validations.

Published in:

Light: Science & Applications, 2024, v. 13, n. 1, p. 1, doi. 10.1038/s41377-024-01475-5

By:

Qi, Yifei;
Ni, Longqun;
Ye, Zhenyu;
Zhang, Jiaojiao;
Bao, Xingyu;
Wang, Pan;
Rao, Yunjiang;
Raposo, Ernesto P.;
Gomes, Anderson S. L.;
Wang, Zinan

Publication type:

Article

In-depth analysis reveals complex molecular aetiology in a cohort of idiopathic cerebral palsy.

Published in:

2022

By:

Li, Na;
Zhou, Pei;
Tang, Hongmei;
He, Lu;
Fang, Xiang;
Zhao, Jinxiang;
Wang, Xin;
Qi, Yifei;
Sun, Chuanbo;
Lin, Yunting;
Qin, Fengying;
Yang, Miaomiao;
Zhang, Zhan;
Liao, Caihua;
Zheng, Shuxin;
Peng, Xiaofang;
Xue, Ting;
Zhu, Qianying;
Li, Hong;
Li, Yan

Publication type:

journal article

Generation of Rational Drug-like Molecular Structures Through a Multiple-Objective Reinforcement Learning Framework.

Published in:

Molecules, 2025, v. 30, n. 1, p. 18, doi. 10.3390/molecules30010018

By:

Zhang, Xiangying;
Gao, Haotian;
Qi, Yifei;
Li, Yan;
Wang, Renxiao

Publication type:

Article

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.

Published in:

Glycobiology, 2019, v. 29, n. 4, p. 320, doi. 10.1093/glycob/cwz003

By:

Park, Sang-Jun;
Lee, Jumin;
Qi, Yifei;
Kern, Nathan R;
Lee, Hui Sun;
Jo, Sunhwan;
Joung, InSuk;
Joo, Keehyung;
Lee, Jooyoung;
Im, Wonpil

Publication type:

Article

Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies.

Published in:

Glycobiology, 2016, v. 26, n. 3, p. 251, doi. 10.1093/glycob/cwv101

By:

Yifei Qi;
Sunhwan Jo;
Wonpil Im

Publication type:

Article

Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.

Published in:

Glycobiology, 2016, v. 26, n. 1, p. 19, doi. 10.1093/glycob/cwv083

By:

Sunhwan Jo;
Yifei Qi;
Wonpil Im

Publication type:

Article

Evaluation of sequence-based predictors for phase-separating protein.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad213

By:

Liao, Shaofeng;
Zhang, Yujun;
Qi, Yifei;
Zhang, Zhuqing

Publication type:

Article

Photo-Induced Holes Initiating Peroxymonosulfate Oxidation for Carbamazepine Degradation via Singlet Oxygen.

Published in:

Catalysts (2073-4344), 2022, v. 12, n. 11, p. 1327, doi. 10.3390/catal12111327

By:

Qi, Yifei;
Zhou, Xiaoyue;
Li, Zhenjie;
Yin, Renli;
Qin, Junhao;
Li, Huashou;
Guo, Wanqian;
Li, Adela Jing;
Qiu, Rongliang

Publication type:

Article

Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq.

Published in:

Biomolecules (2218-273X), 2021, v. 11, n. 11, p. 1653, doi. 10.3390/biom11111653

By:

Li, Mengxin;
Cong, Yalong;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

A novel miR‐82 target PA2G4 and FHL3 checking myocardial ischemia.

Published in:

Clinical & Translational Medicine, 2020, v. 10, n. 5, p. 1, doi. 10.1002/ctm2.179

By:

Kang, Ruixia;
Li, Bing;
Zhang, Yingying;
Liu, Qiong;
Liu, Jun;
Qi, Yifei;
Teng, Fei;
Xu, Huaiqian;
Liu, Zhenhua;
Zhu, Xiaolong;
Qiao, Wangmin;
Tian, Jinzhou;
Wang, Yimin;
Nan, Jingyi;
Guo, Jian;
Wang, Zhong

Publication type:

Article

Testing and Defending Methods Against DOS Attack in State Estimation.

Published in:

Asian Journal of Control, 2017, v. 19, n. 4, p. 1295, doi. 10.1002/asjc.1441

By:

Zhang, Heng;
Qi, Yifei;
Zhou, Huan;
Zhang, Jian;
Sun, Jing

Publication type:

Article