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2020 – today
- 2024
- [j151]Ruofan Jin, Qing Ye
, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang
, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
:
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences. Briefings Bioinform. 25(4) (2024) - [j150]Xing Zhang, Jianbo Tong, Tianhao Wang
, Tianyue Wang, Lei Xu, Zhe Wang
, Tingjun Hou, Peichen Pan
:
Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis. Comput. Biol. Medicine 169: 107815 (2024) - [j149]Tianhao Wang
, Jianbo Tong, Xing Zhang, Zhe Wang
, Lei Xu, Peichen Pan
, Tingjun Hou:
Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain. Comput. Biol. Medicine 174: 108397 (2024) - [j148]Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh:
A general model for predicting enzyme functions based on enzymatic reactions. J. Cheminformatics 16(1): 38 (2024) - [j147]Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang
, Peichen Pan
, Dan Li
, Yafeng Deng, Xiaojun Yao
, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou
:
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. J. Chem. Inf. Model. 64(4): 1213-1228 (2024) - [j146]Huifeng Zhao, Dejun Jiang
, Chao Shen
, Jintu Zhang
, Xujun Zhang, Xiaorui Wang
, Dou Nie, Tingjun Hou
, Yu Kang
:
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. J. Chem. Inf. Model. 64(6): 2112-2124 (2024) - [j145]Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang
, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu
, Tingjun Hou
, Yu Kang
:
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. J. Chem. Inf. Model. 64(9): 3630-3639 (2024) - [j144]Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou:
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. J. Chem. Inf. Model. 64(13): 5016-5027 (2024) - [j143]Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou:
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. J. Chem. Inf. Model. 64(14): 5381-5391 (2024) - [i10]Yiheng Zhu, Zitai Kong, Jialu Wu, Weize Liu, Yuqiang Han, Mingze Yin, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou:
Generative AI for Controllable Protein Sequence Design: A Survey. CoRR abs/2402.10516 (2024) - [i9]Odin Zhang, Yufei Huang, Shichen Cheng, Mengyao Yu, Xujun Zhang, Haitao Lin, Yundian Zeng, Mingyang Wang, Zhenxing Wu, Huifeng Zhao, Zaixi Zhang, Chenqing Hua, Yu Kang, Sunliang Cui, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou:
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. CoRR abs/2404.00014 (2024) - [i8]Lijun Liu, Jiali Yang, Jianfei Song, Xinglin Yang, Lele Niu, Zeqi Cai, Hui Shi, Tingjun Hou, Chang-Yu Hsieh, Weiran Shen, Yafeng Deng:
AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation. CoRR abs/2404.10573 (2024) - [i7]Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Yuansheng Huang, Dejun Jiang, Chang-Yu Hsieh, Peichen Pan, Tingjun Hou:
Deep Lead Optimization: Leveraging Generative AI for Structural Modification. CoRR abs/2404.19230 (2024) - 2023
- [j142]Lei Wang, Shao-Hua Shi
, Hui Li, Xiangxiang Zeng, Su-You Liu, Zhao-Qian Liu, Yafeng Deng, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Reducing false positive rate of docking-based virtual screening by active learning. Briefings Bioinform. 24(1) (2023) - [j141]Dong Wang, Zhenxing Wu, Chao Shen
, Lingjie Bao, Hao Luo, Zhe Wang
, Hucheng Yao, De-Xin Kong
, Cheng Luo
, Tingjun Hou
:
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors. Briefings Bioinform. 24(1) (2023) - [j140]Lingling Wang, Lei Xu, Zhe Wang
, Tingjun Hou
, Haiping Hao, Huiyong Sun
:
Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis. Briefings Bioinform. 24(1) (2023) - [j139]Shukai Gu, Chao Shen
, Jiahui Yu, Hong Zhao, Huanxiang Liu
, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang
, Tingjun Hou
, Yu Kang:
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? Briefings Bioinform. 24(2) (2023) - [j138]Kai-Yue Ji, Chong Liu, Zhao-Qian Liu, Yafeng Deng, Tingjun Hou
, Dong-Sheng Cao
:
Comprehensive assessment of nine target prediction web services: which should we choose for target fishing? Briefings Bioinform. 24(2) (2023) - [j137]Jian Gao, Zheyuan Shen, Yufeng Xie, Jialiang Lu, Yang Lu, Sikang Chen, Qingyu Bian, Yue Guo
, Liteng Shen, Jian Wu, Binbin Zhou
, Tingjun Hou
, Qiaojun He, Jinxin Che, Xiaowu Dong
:
TransFoxMol: predicting molecular property with focused attention. Briefings Bioinform. 24(5) (2023) - [j136]Xujun Zhang, Chao Shen
, Tianyue Wang, Yafeng Deng, Yu Kang
, Dan Li, Tingjun Hou
, Peichen Pan
:
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Briefings Bioinform. 24(5) (2023) - [j135]Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang
:
Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. J. Comput. Chem. 44(13): 1300-1311 (2023) - [j134]Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang
:
Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. J. Comput. Chem. 44(14): 1334-1346 (2023) - [j133]Kexin Chen
, Guangyong Chen, Junyou Li, Yuansheng Huang, Ercheng Wang
, Tingjun Hou, Pheng-Ann Heng:
MetaRF: attention-based random forest for reaction yield prediction with a few trails. J. Cheminformatics 15(1): 43 (2023) - [j132]Su-Qing Yang, Liu-Xia Zhang, You-Jin Ge, Jin-Wei Zhang, Jian-Xin Hu, Cheng-Ying Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences. J. Cheminformatics 15(1): 48 (2023) - [j131]Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan
, Yu Kang:
TB-IECS: an accurate machine learning-based scoring function for virtual screening. J. Cheminformatics 15(1): 63 (2023) - [j130]Teng-Zhi Long
, Shao-Hua Shi
, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu
, Min Li
, Tingjun Hou
, Dong-Sheng Cao
:
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. J. Chem. Inf. Model. 63(1): 111-125 (2023) - [j129]Jintu Zhang
, Haotian Zhang, Zhixin Qin, Yu Kang
, Xin Hong
, Tingjun Hou
:
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. J. Chem. Inf. Model. 63(4): 1133-1142 (2023) - [j128]Yanqing Duan
, Li Fu, Xiao-Chen Zhang, Teng-Zhi Long
, Yuan-Hang He, Zhao-Qian Liu
, Ai-Ping Lu, Yafeng Deng, Chang-Yu Hsieh
, Tingjun Hou
, Dong-Sheng Cao
:
Improved GNNs for Log D7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. J. Chem. Inf. Model. 63(8): 2345-2359 (2023) - [j127]Yuwei Yang, Chang-Yu Hsieh, Yu Kang
, Tingjun Hou
, Huanxiang Liu, Xiaojun Yao:
Deep Generation Model Guided by the Docking Score for Active Molecular Design. J. Chem. Inf. Model. 63(10): 2983-2991 (2023) - [j126]Jike Wang, Yundian Zeng
, Huiyong Sun
, Junmei Wang, Xiaorui Wang
, Ruofan Jin, Mingyang Wang, Xujun Zhang, Dong-Sheng Cao
, Xi Chen, Chang-Yu Hsieh
, Tingjun Hou
:
Molecular Generation with Reduced Labeling through Constraint Architecture. J. Chem. Inf. Model. 63(11): 3319-3327 (2023) - [j125]Haiyi Chen, Yue Guo, Shengqing Ye
, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou
, Hongguang Xia, Yu Kang
, Mojie Duan
:
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J. Chem. Inf. Model. 63(16): 5232-5243 (2023) - [j124]Xiaodan Yin
, Xiaorui Wang
, Yuquan Li, Jike Wang, Yuwei Wang
, Yafeng Deng, Tingjun Hou
, Huanxiang Liu, Pei Luo
, Xiaojun Yao
:
CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. J. Chem. Inf. Model. 63(20): 6169-6176 (2023) - [j123]Zhe Wang, Haiyang Zhong
, Jintu Zhang, Peichen Pan
, Dong Wang, Huanxiang Liu
, Xiaojun Yao
, Tingjun Hou
, Yu Kang
:
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. J. Chem. Inf. Model. 63(21): 6525-6536 (2023) - [j122]Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou
, Haiping Hao, Huiyong Sun
:
Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. J. Chem. Inf. Model. 63(23): 7529-7544 (2023) - [j121]Zhenxing Wu
, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh
, Tingjun Hou
:
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. J. Chem. Inf. Model. 63(24): 7617-7627 (2023) - [j120]Kuerbannisha Amahong, Wei Zhang
, Ying Zhou, Song Zhang
, Jiayi Yin
, Fengcheng Li, Hong-Quan Xu, Tian-Ci Yan, Zi-Xuan Yue, Yu-Hong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han
, Feng Zhu
:
CovInter: interaction data between coronavirus RNAs and host proteins. Nucleic Acids Res. 51(D1): 546-556 (2023) - [j119]Fengcheng Li
, Jiayi Yin
, Mingkun Lu, Minjie Mou
, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang
, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen
, Feng Zhu
:
DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res. 51(D1): 1288-1299 (2023) - [j118]Gaoqi Weng
, Xuanyan Cai, Dong-Sheng Cao
, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
:
PROTAC-DB 2.0: an updated database of PROTACs. Nucleic Acids Res. 51(D1): 1367-1372 (2023) - [j117]Yunxia Wang
, Zhen Chen, Ziqi Pan
, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang
, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
:
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. Nucleic Acids Res. 51(W1): 509-519 (2023) - [j116]Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu
, Chao Shen
, Hanqun Cao, Hongyan Du, Yu Kang
, Yafeng Deng, Furui Liu
, Guangyong Chen
, Chang-Yu Hsieh
, Tingjun Hou
:
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. Nat. Mac. Intell. 5(9): 1020-1030 (2023) - [j115]Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang
, Zhe Wang, Ercheng Wang
, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan
, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou:
Efficient and accurate large library ligand docking with KarmaDock. Nat. Comput. Sci. 3(9): 789-804 (2023) - [j114]Odin Zhang, Tianyue Wang, Gaoqi Weng, Dejun Jiang, Ning Wang, Xiaorui Wang
, Huifeng Zhao, Jialu Wu, Ercheng Wang
, Guangyong Chen, Yafeng Deng, Peichen Pan
, Yu Kang, Chang-Yu Hsieh, Tingjun Hou:
Learning on topological surface and geometric structure for 3D molecular generation. Nat. Comput. Sci. 3(10): 849-859 (2023) - [c3]Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu:
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. IJCAI 2023: 5002-5010 - [c2]Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu:
Sample-efficient Multi-objective Molecular Optimization with GFlowNets. NeurIPS 2023 - [i6]Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Tingjun Hou, Mingli Song:
Recent advances in artificial intelligence for retrosynthesis. CoRR abs/2301.05864 (2023) - [i5]Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu:
Sample-efficient Multi-objective Molecular Optimization with GFlowNets. CoRR abs/2302.04040 (2023) - [i4]Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu:
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. CoRR abs/2305.08457 (2023) - [i3]Yue Wan, Jialu Wu, Tingjun Hou, Chang-Yu Hsieh, Xiaowei Jia:
From molecules to scaffolds to functional groups: building context-dependent molecular representation via multi-channel learning. CoRR abs/2311.02798 (2023) - [i2]Hongyan Du, Guo-Wei Wei, Tingjun Hou:
Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing. CoRR abs/2312.01272 (2023) - 2022
- [j113]Mingyang Wang, Huiyong Sun
, Jike Wang, Jinping Pang, Xin Chai, Lei Xu, Honglin Li, Dongsheng Cao
, Tingjun Hou
:
Comprehensive assessment of deep generative architectures for de novo drug design. Briefings Bioinform. 23(1) (2022) - [j112]Dejun Jiang, Huiyong Sun
, Jike Wang, Chang-Yu Hsieh, Yuquan Li
, Zhenxing Wu, Dong-Sheng Cao
, Jian Wu, Tingjun Hou
:
Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning. Briefings Bioinform. 23(2) (2022) - [j111]Xiao-Chen Zhang
, Jia-Cai Yi
, Guo-Ping Yang, Chengkun Wu, Tingjun Hou
, Dong-Sheng Cao
:
ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images. Briefings Bioinform. 23(2) (2022) - [j110]Rongfan Tang, Pengcheng Chen, Zhe Wang
, Lingling Wang, Haiping Hao, Tingjun Hou
, Huiyong Sun
:
Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. Briefings Bioinform. 23(3) (2022) - [j109]Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Chang-Yu Hsieh, Dongsheng Cao
, Tingjun Hou
:
Knowledge-based BERT: a method to extract molecular features like computational chemists. Briefings Bioinform. 23(3) (2022) - [j108]Zhe Wang
, Hong Pan, Huiyong Sun
, Yu Kang, Huanxiang Liu, Dongsheng Cao
, Tingjun Hou
:
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. Briefings Bioinform. 23(5) (2022) - [j107]Jia-Cai Yi
, Chengkun Wu
, Xiao-Chen Zhang, Xinyi Xiao, Yanlong Qiu
, Wentao Zhao, Tingjun Hou
, Dong-Sheng Cao
:
MICER: a pre-trained encoder-decoder architecture for molecular image captioning. Bioinform. 38(19): 4562-4572 (2022) - [j106]Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong
, Zi-Yi Yang, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
:
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes. J. Cheminformatics 14(1): 23 (2022) - [j105]Yang Yu, Zhe Wang
, Lingling Wang, Sheng Tian
, Tingjun Hou, Huiyong Sun
:
Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses. J. Cheminformatics 14(1): 56 (2022) - [j104]Gaoang Wang, Jiahui Yu, Hongyan Du, Chao Shen, Xujun Zhang, Yifei Liu, Yangyang Zhang, Dong-Sheng Cao
, Peichen Pan
, Tingjun Hou:
VGSC-DB: an online database of voltage-gated sodium channels. J. Cheminformatics 14(1): 75 (2022) - [j103]Mingyang Wang, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan
, Dan Li, Yafeng Deng, Honglin Li, Chang-Yu Hsieh, Tingjun Hou:
ReMODE: a deep learning-based web server for target-specific drug design. J. Cheminformatics 14(1): 84 (2022) - [j102]Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang
, Dong-Sheng Cao
, Zhe Wang
, Tingjun Hou
:
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. J. Chem. Inf. Model. 62(12): 2973-2986 (2022) - [j101]Yuwei Yang, Zhenxing Wu
, Xiaojun Yao
, Yu Kang
, Tingjun Hou
, Chang-Yu Hsieh, Huanxiang Liu
:
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. J. Chem. Inf. Model. 62(13): 3191-3199 (2022) - [j100]Qinghua Wang, Zhe Wang
, Sheng Tian
, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou
, Haiping Hao, Huiyong Sun
:
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. J. Chem. Inf. Model. 62(17): 3993-4007 (2022) - [j99]Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan
, Tingjun Hou
:
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. J. Chem. Inf. Model. 62(21): 5233-5245 (2022) - [j98]Jialu Wu, Junmei Wang
, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang
, Dong-Sheng Cao
, Chang-Yu Hsieh
, Tingjun Hou
:
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. J. Chem. Inf. Model. 62(23): 5975-5987 (2022) - [j97]Guo-Li Xiong
, Zhi-Jiang Yang, Jia-Cai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou
, Dongsheng Cao
:
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. Nucleic Acids Res. 50(D1): 1200-1207 (2022) - [i1]Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Min Wu, Tingjun Hou, Mingli Song:
Root-aligned SMILES for Molecular Retrosynthesis Prediction. CoRR abs/2203.11444 (2022) - 2021
- [j96]Jie Dong, Min-Feng Zhu, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
:
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. Briefings Bioinform. 22(1): 474-484 (2021) - [j95]Chao Shen, Ye Hu, Zhe Wang
, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng Cao
, Tingjun Hou:
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. Briefings Bioinform. 22(1): 497-514 (2021) - [j94]Chao Shen, Ye Hu, Zhe Wang
, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dong-Sheng Cao
, Tingjun Hou:
Beware of the generic machine learning-based scoring functions in structure-based virtual screening. Briefings Bioinform. 22(3) (2021) - [j93]Jike Wang, Dong-Sheng Cao
, Cunchen Tang, Lei Xu, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun
, Tingjun Hou:
DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges. Briefings Bioinform. 22(3) (2021) - [j92]Guo-Li Xiong
, Wenling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
:
Improving structure-based virtual screening performance via learning from scoring function components. Briefings Bioinform. 22(3) (2021) - [j91]Zi-Yi Yang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
:
Scopy: an integrated negative design python library for desirable HTS/VS database design. Briefings Bioinform. 22(3) (2021) - [j90]Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei
, Chao Shen, Dejun Jiang, Zhe Wang
, Dong-Sheng Cao
, Tingjun Hou:
Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets. Briefings Bioinform. 22(4) (2021) - [j89]Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Mingzhu Yin
, Hong-Li Jiang, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
:
ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. Briefings Bioinform. 22(4) (2021) - [j88]Li Fu, Zi-Yi Yang, Zhi-Jiang Yang, Ming-Zhu Yin
, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
:
QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. Briefings Bioinform. 22(5) (2021) - [j87]Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang
, Dong-Sheng Cao
, Tingjun Hou
:
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? Briefings Bioinform. 22(5) (2021) - [j86]Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Dong-Sheng Cao
, Tingjun Hou:
Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. Briefings Bioinform. 22(5) (2021) - [j85]Zi-Yi Yang, Zhi-Jiang Yang, Yue Zhao, Ming-Zhu Yin
, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou
, Dong-Sheng Cao
:
PySmash: Python package and individual executable program for representative substructure generation and application. Briefings Bioinform. 22(5) (2021) - [j84]Qing Ye
, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li, Dong-Sheng Cao
, Tingjun Hou
:
Identification of active molecules against Mycobacterium tuberculosis through machine learning. Briefings Bioinform. 22(5) (2021) - [j83]Chengkun Wu, Xiao-Chen Zhang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. Briefings Bioinform. 22(6) (2021) - [j82]Xiao-Chen Zhang, Chengkun Wu
, Zhi-Jiang Yang, Zhen-Xing Wu, Jia-Cai Yi, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao
:
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. Briefings Bioinform. 22(6) (2021) - [j81]Jike Wang, Huiyong Sun
, Jiawen Chen, Dejun Jiang, Zhe Wang
, Zhenxing Wu, Xi Chen, Dong-Sheng Cao, Tingjun Hou
:
DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms. Bioinform. 37(22): 4255-4257 (2021) - [j80]Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang
, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dong-Sheng Cao
, Tingjun Hou
:
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. J. Cheminformatics 13(1): 6 (2021) - [j79]Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang
, Chao Shen, Dong-Sheng Cao
, Jian Wu, Tingjun Hou
:
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models. J. Cheminformatics 13(1): 12 (2021) - [j78]Chao Shen, Xueping Hu
, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang
, Lei Xu, Yu Kang, Dong-Sheng Cao
, Tingjun Hou
:
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. J. Cheminformatics 13(1): 81 (2021) - [j77]Zi-Yi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Tingjun Hou, Dong-Sheng Cao
:
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. J. Cheminformatics 13(1): 86 (2021) - [j76]Ercheng Wang
, Weitao Fu
, Dejun Jiang
, Huiyong Sun
, Junmei Wang
, Xujun Zhang, Gaoqi Weng, Hui Liu
, Peng Tao, Tingjun Hou
:
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. J. Chem. Inf. Model. 61(6): 2844-2856 (2021) - [j75]Hongyan Du
, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao
, Tingjun Hou
:
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic Acids Res. 49(Database-Issue): D1122-D1129 (2021) - [j74]Gaoqi Weng, Chao Shen, Dong-Sheng Cao
, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou
:
PROTAC-DB: an online database of PROTACs. Nucleic Acids Res. 49(Database-Issue): D1381-D1387 (2021) - [j73]Guo-Li Xiong
, Zhenxing Wu, Jia-Cai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin
, Xiangxiang Zeng
, Chengkun Wu
, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
:
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 49(Webserver-Issue): 5-14 (2021) - [j72]Jike Wang, Chang-Yu Hsieh, Mingyang Wang, Xiaorui Wang, Zhenxing Wu, Dejun Jiang, Benben Liao, Xujun Zhang, Bo Yang, Qiaojun He, Dongsheng Cao
, Xi Chen, Tingjun Hou
:
Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning. Nat. Mach. Intell. 3(10): 914-922 (2021) - 2020
- [j71]Chao Shen, Zhe Wang
, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang
, Lei Xu, Feng Zhu
, Dan Li, Tingjun Hou:
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Briefings Bioinform. 21(1): 282-297 (2020) - [j70]Jike Wang, Dong-Sheng Cao
, Cunchen Tang, Xi Chen, Huiyong Sun
, Tingjun Hou:
Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning. Bioinform. 36(18): 4721-4728 (2020) - [j69]Dejun Jiang, Tailong Lei, Zhe Wang
, Chao Shen, Dong-Sheng Cao
, Tingjun Hou
:
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. J. Cheminformatics 12(1): 16 (2020) - [j68]Li Fu, Lu Liu, Zhi-Jiang Yang, Pan Li, Jun-Jie Ding, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. J. Chem. Inf. Model. 60(1): 63-76 (2020) - [j67]Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. J. Chem. Inf. Model. 60(4): 2031-2043 (2020) - [j66]Wenling Ye, Chao Shen, Guo-Li Xiong
, Jun-Jie Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
:
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. J. Chem. Inf. Model. 60(9): 4216-4230 (2020) - [j65]Ercheng Wang
, Hui Liu
, Junmei Wang
, Gaoqi Weng, Huiyong Sun
, Zhe Wang
, Yu Kang, Tingjun Hou
:
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. J. Chem. Inf. Model. 60(11): 5353-5365 (2020)
2010 – 2019
- 2019
- [j64]Zhe Wang
, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang
, Dan Li, Yu Kang
, Feng Zhu
, Tingjun Hou:
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinform. 35(10): 1777-1779 (2019) - [j63]Ye Jin, Mojie Duan
, Xuwen Wang, Xiaotian Kong, Wenfang Zhou, Huiyong Sun
, Hui Liu, Dan Li, Huidong Yu, Youyong Li
, Tingjun Hou
:
Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 59(2): 842-857 (2019) - [j62]Zi-Yi Yang, Zhi-Jiang Yang, Jie Dong, Liang-Liang Wang, Liu-Xia Zhang, Jun-Jie Ding, Xiao-Qin Ding, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery. J. Chem. Inf. Model. 59(9): 3714-3726 (2019) - [j61]Zhenxing Wu, Tailong Lei
, Chao Shen, Zhe Wang
, Dong-Sheng Cao
, Tingjun Hou
:
ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches. J. Chem. Inf. Model. 59(11): 4587-4601 (2019) - [j60]Gaoqi Weng
, Ercheng Wang
, Zhe Wang
, Hui Liu, Feng Zhu
, Dan Li, Tingjun Hou:
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Res. 47(Webserver-Issue): W322-W330 (2019) - 2018
- [j59]Wenfang Zhou
, Mojie Duan
, Weitao Fu
, Jinping Pang
, Qin Tang
, Huiyong Sun
, Lei Xu
, Shan Chang
, Dan Li
, Tingjun Hou
:
Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays. Genom. Proteom. Bioinform. 16(6): 416-427 (2018) - [j58]Jun Shang
, Ben Hu, Junmei Wang
, Feng Zhu
, Yu Kang
, Dan Li, Huiyong Sun
, De-Xin Kong
, Tingjun Hou
:
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. J. Chem. Inf. Model. 58(6): 1182-1193 (2018) - [j57]Na Liu, Wenfang Zhou, Yue Guo, Junmei Wang
, Weitao Fu
, Huiyong Sun
, Dan Li, Mojie Duan
, Tingjun Hou:
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator. J. Chem. Inf. Model. 58(8): 1652-1661 (2018) - 2017
- [j56]Jun Shang
, Huiyong Sun
, Hui Liu, Fu Chen, Sheng Tian
, Peichen Pan
, Dan Li, De-Xin Kong
, Tingjun Hou:
Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. J. Cheminformatics 9(1): 25:1-25:16 (2017) - [j55]Ting Feng, Fu Chen, Yu Kang
, Huiyong Sun
, Hui Liu, Dan Li, Feng Zhu
, Tingjun Hou:
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J. Cheminformatics 9(1): 66:1-66:15 (2017) - [j54]Sheng Tian
, Xu Wang, Linlang Li, Xiaohu Zhang, Youyong Li
, Feng Zhu
, Tingjun Hou
, Xuechu Zhen
:
Discovery of Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening. J. Chem. Inf. Model. 57(6): 1474-1487 (2017) - [j53]Huiyong Sun
, Youyong Li
, Mingyun Shen, Dan Li, Yu Kang
, Tingjun Hou
:
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. J. Chem. Inf. Model. 57(8): 1895-1906 (2017) - 2016
- [j52]Hui Liu, Tingjun Hou:
CaFE: a tool for binding affinity prediction using end-point free energy methods. Bioinform. 32(14): 2216-2218 (2016) - [j51]Tailong Lei
, Youyong Li, Yunlong Song, Dan Li, Huiyong Sun, Tingjun Hou:
ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling. J. Cheminformatics 8(1): 6:1-6:19 (2016) - 2015
- [j50]Nan Li, Richard I. Ainsworth
, Bo Ding, Tingjun Hou, Wei Wang:
Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. J. Chem. Inf. Model. 55(7): 1400-1412 (2015) - [j49]Yu Zhang, Lei Xu, Zhiqiang Zhang, Zhiyu Zhang, Longtai Zheng, Dan Li, Youyong Li, Feng Liu, Kunqian Yu, Tingjun Hou, Xuechu Zhen
:
Structure-Activity Relationships and Anti-inflammatory Activities of N-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors. J. Chem. Inf. Model. 55(9): 1994-2004 (2015) - [j48]Peichen Pan
, Sheng Tian
, Huiyong Sun, Xiaotian Kong, Wenfang Zhou, Dan Li, Youyong Li, Tingjun Hou:
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. J. Chem. Inf. Model. 55(12): 2693-2704 (2015) - 2014
- [j47]Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang
, Jian Zhang
, Tingjun Hou:
MORT: a powerful foundational library for computational biology and CADD. J. Cheminformatics 6(1): 36 (2014) - [j46]Sheng Tian
, Huiyong Sun, Peichen Pan
, Dan Li, Xuechu Zhen
, Youyong Li, Tingjun Hou:
Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility. J. Chem. Inf. Model. 54(10): 2664-2679 (2014) - [j45]Huiyong Sun, Youyong Li
, Sheng Tian
, Junmei Wang
, Tingjun Hou:
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape. PLoS Comput. Biol. 10(7) (2014) - 2013
- [j44]Wenkang Huang, Shaoyong Lu, Zhimin Huang
, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang
:
Allosite: a method for predicting allosteric sites. Bioinform. 29(18): 2357-2359 (2013) - [j43]Sheng Tian
, Youyong Li
, Junmei Wang
, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou:
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. J. Cheminformatics 5: 5 (2013) - [j42]Shunye Zhou, Youyong Li
, Tingjun Hou:
Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors. J. Chem. Inf. Model. 53(4): 982-996 (2013) - [j41]Peichen Pan
, Youyong Li
, Huidong Yu, Huiyong Sun, Tingjun Hou:
Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches. J. Chem. Inf. Model. 53(4): 997-1006 (2013) - [j40]Wei Cui, Yuanhua Cheng, Lingling Geng, Den-Sheng Liang, Tingjun Hou, Mingjuan Ji:
Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling. J. Chem. Inf. Model. 53(5): 1157-1167 (2013) - [j39]Sheng Tian
, Youyong Li
, Dan Li, Xiaojie Xu, Junmei Wang
, Qian Zhang, Tingjun Hou:
Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design. J. Chem. Inf. Model. 53(7): 1787-1803 (2013) - [j38]Qian Zhang, Junmei Wang
, Ginés D. Guerrero, José M. Cecilia
, José M. García, Youyong Li
, Horacio Emilio Pérez Sánchez
, Tingjun Hou:
Accelerated Conformational Entropy Calculations Using Graphic Processing Units. J. Chem. Inf. Model. 53(8): 2057-2064 (2013) - [j37]Huiyong Sun, Youyong Li
, Dan Li, Tingjun Hou:
Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches. J. Chem. Inf. Model. 53(9): 2376-2389 (2013) - [j36]Sheng Tian
, Huiyong Sun, Youyong Li
, Peichen Pan
, Dan Li, Tingjun Hou:
Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures. J. Chem. Inf. Model. 53(10): 2743-2756 (2013) - [c1]Qian Zhang, José M. García, Junmei Wang, Tingjun Hou, Horacio Emilio Pérez Sánchez:
A GPU based Conformational Entropy Calculation Method. IWBBIO 2013: 735-743 - 2012
- [j35]Qian Zhang, Wei Zhang, Youyong Li
, Junmei Wang
, Liling Zhang, Tingjun Hou:
A rule-based algorithm for automatic bond type perception. J. Cheminformatics 4: 26 (2012) - [j34]Mingyun Shen, Sheng Tian
, Youyong Li
, Qian Li, Xiaojie Xu, Junmei Wang
, Tingjun Hou:
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. J. Cheminformatics 4: 31 (2012) - [j33]Zhiwei Feng, Tingjun Hou, Youyong Li
:
Studies on the Interactions between β2 Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations. J. Chem. Inf. Model. 52(4): 1005-1014 (2012) - [j32]Dongyue Cao, Junmei Wang
, Rui Zhou, Youyong Li
, Huidong Yu, Tingjun Hou:
ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs. J. Chem. Inf. Model. 52(5): 1132-1137 (2012) - [j31]Junmei Wang
, Tingjun Hou:
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations. J. Chem. Inf. Model. 52(5): 1199-1212 (2012) - [j30]Zhiwei Feng, Tingjun Hou, Youyong Li
:
Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations. J. Chem. Inf. Model. 52(8): 2119-2131 (2012) - [j29]Lin Li, Youyong Li
, Liling Zhang, Tingjun Hou:
Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. J. Chem. Inf. Model. 52(10): 2715-2729 (2012) - 2011
- [j28]Tingjun Hou, Youyong Li
, Wei Wang:
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. Bioinform. 27(13): 1814-1821 (2011) - [j27]Tingjun Hou, Junmei Wang
, Youyong Li
, Wei Wang:
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. J. Comput. Chem. 32(5): 866-877 (2011) - [j26]Junmei Wang
, Tingjun Hou:
Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient. J. Comput. Chem. 32(16): 3505-3519 (2011) - [j25]Tingjun Hou, Junmei Wang
, Youyong Li
, Wei Wang:
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. J. Chem. Inf. Model. 51(1): 69-82 (2011) - 2010
- [j24]Junmei Wang
, Tingjun Hou:
Drug and Drug Candidate Building Block Analysis. J. Chem. Inf. Model. 50(1): 55-67 (2010) - [j23]Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji:
Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells. J. Chem. Inf. Model. 50(3): 380-387 (2010) - [j22]Yaxue Zhao, Xuefeng Lu, Chao-Yie Yang, Zhimin Huang
, Wei Fu, Tingjun Hou, Jian Zhang
:
Computational Modeling Toward Understanding Agonist Binding on Dopamine 3. J. Chem. Inf. Model. 50(9): 1633-1643 (2010)
2000 – 2009
- 2009
- [j21]Junmei Wang
, Tingjun Hou, Xiaojie Xu:
Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas. J. Chem. Inf. Model. 49(3): 571-581 (2009) - 2007
- [j20]William A. McLaughlin
, Ken Chen
, Tingjun Hou, Wei Wang:
On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinform. 8 (2007) - [j19]Tingjun Hou, Junmei Wang
, Wei Zhang, Xiaojie Xu:
ADME Evaluation in Drug Discovery, 7. Prediction of Oral Absorption by Correlation and Classification. J. Chem. Inf. Model. 47(1): 208-218 (2007) - [j18]Tingjun Hou, Junmei Wang
, Wei Zhang, Xiaojie Xu:
ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules? J. Chem. Inf. Model. 47(2): 460-463 (2007) - [j17]Junmei Wang
, George Krudy, Tingjun Hou, Wei Zhang, George Holland, Xiaojie Xu:
Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis. J. Chem. Inf. Model. 47(4): 1395-1404 (2007) - [j16]Tingjun Hou, Junmei Wang
, Youyong Li
:
ADME Evaluation in Drug Discovery, 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine. J. Chem. Inf. Model. 47(6): 2408-2415 (2007) - 2006
- [j15]Tingjun Hou, Ken Chen
, William A. McLaughlin
, Benzhuo Lu, Wei Wang:
Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain. PLoS Comput. Biol. 2(1) (2006) - 2005
- [j14]Wei Zhang, Tingjun Hou, Xiaojie Xu:
New Born Radii Deriving Method for Generalized Born Model. J. Chem. Inf. Model. 45(1): 88-93 (2005) - 2004
- [j13]Tingjun Hou, Ke Xia
, Wei Zhang, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach. J. Chem. Inf. Model. 44(1): 266-275 (2004) - [j12]Tingjun Hou, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors [J. Chem. Inf. Comput. Sci. 43, 2137-2152 (2003)]. J. Chem. Inf. Model. 44(2): 766-770 (2004) - [j11]Tingjun Hou, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas [J. Chem. Inf. Comput. Sci. 1058-1067(2003)]. J. Chem. Inf. Model. 44(4): 1516 (2004) - [j10]Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu:
Some Basic Data Structures and Algorithms for Chemical Generic Programming. J. Chem. Inf. Model. 44(5): 1571-1575 (2004) - [j9]Tingjun Hou, Wei Zhang, Ke Xia
, Xuebin Qiao, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties. J. Chem. Inf. Model. 44(5): 1585-1600 (2004) - 2003
- [j8]Tingjun Hou, Lili Zhu, Lirong Chen, Xiaojie Xu:
Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies. J. Chem. Inf. Comput. Sci. 43(1): 273-287 (2003) - [j7]Tingjun Hou, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas. J. Chem. Inf. Comput. Sci. 43(3): 1058-1067 (2003) - [j6]Tingjun Hou, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors. J. Chem. Inf. Comput. Sci. 43(6): 2137-2152 (2003) - 2002
- [j5]Tingjun Hou, Wei Zhang, Xiaojie Xu:
Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics. J. Comput. Aided Mol. Des. 16(1): 27-41 (2002) - [j4]Xuebin Qiao, Tingjun Hou, Wei Zhang, SenLi Guo, Xiaojie Xu:
A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs. J. Chem. Inf. Comput. Sci. 42(3): 481-489 (2002) - 2001
- [j3]Lili Zhu, Tingjun Hou, Lirong Chen, Xiaojie Xu:
3D QSAR Analyses of Novel Tyrosine Kinase Inhibitors Based on Pharmacophore Alignment. J. Chem. Inf. Comput. Sci. 41(4): 1032-1040 (2001) - 2000
- [j2]Tingjun Hou, Z. M. Li, Z. Li, J. Liu, Xiaojie Xu:
Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis. J. Chem. Inf. Comput. Sci. 40(4): 1002-1009 (2000)
1990 – 1999
- 1999
- [j1]Tingjun Hou, Junmei Wang
, N. Liao, Xiaojie Xu:
Applications of Genetic Algorithms on the Structure-Activity Relationship Analysis of Some Cinnamamides. J. Chem. Inf. Comput. Sci. 39(5): 775-781 (1999)
Coauthor Index
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