ADME Evaluation in Drug Discovery, 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine. - Tingjun Hou; Junmei Wang; Youyong Li (J. Chem. Inf. Model., 2007)

Prediction of the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design. - Youyong Li; William A. Goddard III (Pacific Symposium on Biocomputing, 2008)

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. - Tingjun Hou; Youyong Li; Wei Wang 051 (Bioinform., 2011)

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Comput. Chem., 2011)

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Chem. Inf. Model., 2011)

Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors. - Soo-Kyung Kim; Youyong Li; Ravinder Abrol; Jiyoung Heo; William A. Goddard III (J. Chem. Inf. Model., 2011)

Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines. - Mingyun Shen; Sheng Tian; Youyong Li; Qian Li; Xiaojie Xu; Junmei Wang; Tingjun Hou (J. Cheminformatics, 2012)

A rule-based algorithm for automatic bond type perception. - Qian Zhang 063; Wei Zhang 019; Youyong Li; Junmei Wang; Liling Zhang; Tingjun Hou (J. Cheminformatics, 2012)

ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs. - Dongyue Cao; Junmei Wang; Rui Zhou; Youyong Li; Huidong Yu; Tingjun Hou (J. Chem. Inf. Model., 2012)

Studies on the Interactions between β2 Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations. - Zhiwei Feng; Tingjun Hou; Youyong Li (J. Chem. Inf. Model., 2012)

Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations. - Zhiwei Feng; Tingjun Hou; Youyong Li (J. Chem. Inf. Model., 2012)

Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. - Lin Li; Youyong Li; Liling Zhang; Tingjun Hou (J. Chem. Inf. Model., 2012)

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines. - Sheng Tian; Youyong Li; Junmei Wang; Xiaojie Xu; Lei Xu 035; Xiaohong Wang; Lei Chen; Tingjun Hou (J. Cheminformatics, 2013)

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches. - Peichen Pan; Youyong Li; Huidong Yu; Huiyong Sun; Tingjun Hou (J. Chem. Inf. Model., 2013)

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches. - Huiyong Sun; Youyong Li; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design. - Sheng Tian; Youyong Li; Dan Li 013; Xiaojie Xu; Junmei Wang; Qian Zhang 063; Tingjun Hou (J. Chem. Inf. Model., 2013)

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures. - Sheng Tian; Huiyong Sun; Youyong Li; Peichen Pan; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Accelerated Conformational Entropy Calculations Using Graphic Processing Units. - Qian Zhang 063; Junmei Wang; Ginés D. Guerrero; José M. Cecilia; José M. García 001; Youyong Li; Horacio Emilio Pérez Sánchez; Tingjun Hou (J. Chem. Inf. Model., 2013)

Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors. - Shunye Zhou; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2013)

MORT: a powerful foundational library for computational biology and CADD. - Qian Zhang 063; Wei Zhang 019; Youyong Li; Junmei Wang; Jian Zhang 037; Tingjun Hou (J. Cheminformatics, 2014)

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility. - Sheng Tian; Huiyong Sun; Peichen Pan; Dan Li 013; Xuechu Zhen; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2014)

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape. - Huiyong Sun; Youyong Li; Sheng Tian; Junmei Wang; Tingjun Hou (PLoS Comput. Biol., 2014)

Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models. - Peichen Pan; Sheng Tian; Huiyong Sun; Xiaotian Kong; Wenfang Zhou; Dan Li 013; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2015)

Structure-Activity Relationships and Anti-inflammatory Activities of N-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors. - Yu Zhang; Lei Xu 035; Zhiqiang Zhang; Zhiyu Zhang; Longtai Zheng; Dan Li 013; Youyong Li; Feng Liu; Kunqian Yu; Tingjun Hou; Xuechu Zhen (J. Chem. Inf. Model., 2015)

ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling. - Tailong Lei; Youyong Li; Yunlong Song; Dan Li 013; Huiyong Sun; Tingjun Hou (J. Cheminformatics, 2016)

Discovery of Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening. - Sheng Tian; Xu Wang; Linlang Li; Xiaohu Zhang; Youyong Li; Feng Zhu 004; Tingjun Hou; Xuechu Zhen (J. Chem. Inf. Model., 2017)

Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. - Huiyong Sun; Youyong Li; Mingyun Shen; Dan Li 013; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2017)

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. - Zhe Wang 041; Xuwen Wang; Youyong Li; Tailong Lei; Ercheng Wang; Dan Li 013; Yu Kang 002; Feng Zhu 004; Tingjun Hou (Bioinform., 2019)

Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. - Ye Jin; Mojie Duan; Xuwen Wang; Xiaotian Kong; Wenfang Zhou; Huiyong Sun; Hui Liu; Dan Li 013; Huidong Yu; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2019)

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. - Chao Shen 008; Zhe Wang 041; Xiaojun Yao; Youyong Li; Tailong Lei; Ercheng Wang; Lei Xu 035; Feng Zhu 004; Dan Li 013; Tingjun Hou (Briefings Bioinform., 2020)