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Niu Huang, Ph.D. - Publications

Affiliations: 
2007- NIBS, Beijing 
Area:
Computer-aided Drug Design, Computational Chemistry
Website:
http://www.huanglab.org.cn/
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Wang Q, Fu X, Yan Y, Liu T, Xie Y, Song X, Zhou Y, Xu M, Wang P, Fu P, Huang J, Huang N. Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. Journal of Chemical Information and Modeling. PMID 38215394 DOI: 10.1021/acs.jcim.3c01282  0.364
2024 Li X, Shen C, Zhu H, Yang Y, Wang Q, Yang J, Huang N. A High-Quality Data Set of Protein-Ligand Binding Interactions Via Comparative Complex Structure Modeling. Journal of Chemical Information and Modeling. PMID 38181418 DOI: 10.1021/acs.jcim.3c01170  0.667
2023 Nie Y, Qiu Z, Chen S, Chen Z, Song X, Ma Y, Huang N, Cyster JG, Zheng S. Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive G signaling. Nature Communications. 14: 5901. PMID 37737235 DOI: 10.1038/s41467-023-41654-3  0.473
2023 Wang Q, Meng F, Xie Y, Wang W, Meng Y, Li L, Liu T, Qi J, Ni X, Zheng S, Huang J, Huang N. In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. Acs Central Science. 9: 252-265. PMID 36844485 DOI: 10.1021/acscentsci.2c01190  0.345
2022 Zhu H, Zhang Y, Li W, Huang N. A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years. International Journal of Molecular Sciences. 23. PMID 36555602 DOI: 10.3390/ijms232415961  0.36
2022 Xu M, Shen C, Yang J, Wang Q, Huang N. Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening. Acs Omega. 7: 39417-39428. PMID 36340123 DOI: 10.1021/acsomega.2c05826  0.656
2022 Zhu H, Yang J, Huang N. Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening. Journal of Chemical Information and Modeling. PMID 36268980 DOI: 10.1021/acs.jcim.2c01149  0.652
2022 Teng X, Chen S, Wang Q, Chen Z, Wang X, Huang N, Zheng S. Structural insights into G protein activation by D1 dopamine receptor. Science Advances. 8: eabo4158. PMID 35687690 DOI: 10.1126/sciadv.abo4158  0.416
2021 Chen J, Liu N, Huang Y, Wang Y, Sun Y, Wu Q, Li D, Gao S, Wang HW, Huang N, Qi X, Wang X. Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nature Communications. 12: 6204. PMID 34707099 DOI: 10.1038/s41467-021-26546-8  0.309
2020 Yang J, Shen C, Huang N. Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets. Frontiers in Pharmacology. 11: 69. PMID 32161539 DOI: 10.3389/fphar.2020.00069  0.661
2019 Li G, Li W, Xie Y, Wan X, Zheng G, Huang N, Zhou Y. Discovery of Novel Pim-1 Kinase Inhibitors with a Flexible-Receptor Docking Protocol. Journal of Chemical Information and Modeling. PMID 31609618 DOI: 10.1021/acs.jcim.9b00494  0.311
2018 Wang Y, Du Y, Huang N. A survey of the role of nitrile groups in protein-ligand interactions. Future Medicinal Chemistry. PMID 30518255 DOI: 10.4155/Fmc-2018-0252  0.301
2017 Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X, Huang N. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. Journal of Medicinal Chemistry. PMID 28945083 DOI: 10.1021/Acs.Jmedchem.7B01075  0.377
2016 Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angewandte Chemie (International Ed. in English). PMID 27762087 DOI: 10.1002/Anie.201608827  0.361
2015 Zhou Y, Ma J, Lin X, Huang XP, Wu K, Huang N. Structure-Based Discovery of Novel and Selective 5-Hydroxytryptamine 2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome. Journal of Medicinal Chemistry. PMID 26700945 DOI: 10.1021/Acs.Jmedchem.5B01631  0.404
2015 Cao R, Wang Y, Huang N. Discovery of 2-Acylaminothiophene-3-Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules. Journal of Chemical Information and Modeling. PMID 26501568 DOI: 10.1021/Acs.Jcim.5B00540  0.431
2015 Zhou Y, Huang N. Binding site druggability assessment in fragment-based drug design. Methods in Molecular Biology (Clifton, N.J.). 1289: 13-21. PMID 25709029 DOI: 10.1007/978-1-4939-2486-8_2  0.414
2014 Yao Q, Zhang L, Wan X, Chen J, Hu L, Ding X, Li L, Karar J, Peng H, Chen S, Huang N, Rauscher FJ, Shao F. Structure and specificity of the bacterial cysteine methyltransferase effector NleE suggests a novel substrate in human DNA repair pathway. Plos Pathogens. 10: e1004522. PMID 25412445 DOI: 10.1371/Journal.Ppat.1004522  0.405
2014 Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, Shao F. A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Elife. 3. PMID 25310236 DOI: 10.7554/Elife.03714  0.328
2014 Cao R, Huang N, Wang Y. Evaluation and application of MD-PB/SA in structure-based hierarchical virtual screening. Journal of Chemical Information and Modeling. 54: 1987-96. PMID 24977649 DOI: 10.1021/Ci5003203  0.503
2014 Deng M, Lu Z, Zheng J, Wan X, Chen X, Hirayasu K, Sun H, Lam Y, Chen L, Wang Q, Song C, Huang N, Gao GF, Jiang Y, Arase H, et al. A motif in LILRB2 critical for Angptl2 binding and activation. Blood. 124: 924-35. PMID 24899623 DOI: 10.1182/Blood-2014-01-549162  0.361
2014 Sun H, Zhao L, Peng S, Huang N. Incorporating replacement free energy of binding-site waters in molecular docking. Proteins. 82: 1765-76. PMID 24549784 DOI: 10.1002/Prot.24530  0.428
2014 Li W, Wan X, Zeng F, Xie Y, Wang Y, Zhang W, Li L, Huang N. More than just a GPCR ligand: structure-based discovery of thioridazine derivatives as Pim-1 kinase inhibitors Med. Chem. Commun.. 5: 507-511. DOI: 10.1039/C4Md00030G  0.432
2013 Cao R, Li W, Sun HZ, Zhou Y, Huang N. [Computational chemistry in structure-based drug design]. Yao Xue Xue Bao = Acta Pharmaceutica Sinica. 48: 1041-52. PMID 24133970  0.324
2013 Wan X, Ma Y, McClendon CL, Huang LJ, Huang N. Ab initio modeling and experimental assessment of Janus Kinase 2 (JAK2) kinase-pseudokinase complex structure. Plos Computational Biology. 9: e1003022. PMID 23592968 DOI: 10.1371/Journal.Pcbi.1003022  0.361
2013 Wan X, Zhang W, Li L, Xie Y, Li W, Huang N. A new target for an old drug: identifying mitoxantrone as a nanomolar inhibitor of PIM1 kinase via kinome-wide selectivity modeling. Journal of Medicinal Chemistry. 56: 2619-29. PMID 23442188 DOI: 10.1021/Jm400045Y  0.337
2012 Yao Q, Cui J, Wang J, Li T, Wan X, Luo T, Gong YN, Xu Y, Huang N, Shao F. Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Proceedings of the National Academy of Sciences of the United States of America. 109: 20395-400. PMID 23175788 DOI: 10.1073/Pnas.1210831109  0.369
2012 Cao R, Liu M, Yin M, Liu Q, Wang Y, Huang N. Discovery of novel tubulin inhibitors via structure-based hierarchical virtual screening. Journal of Chemical Information and Modeling. 52: 2730-40. PMID 22992059 DOI: 10.1021/Ci300302C  0.485
2012 Lin X, Huang XP, Chen G, Whaley R, Peng S, Wang Y, Zhang G, Wang SX, Wang S, Roth BL, Huang N. Life beyond kinases: structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors. Journal of Medicinal Chemistry. 55: 5749-59. PMID 22694093 DOI: 10.1021/Jm300338M  0.33
2012 Peng S, Lin X, Guo Z, Huang N. Identifying multiple-target ligands via computational chemogenomics approaches. Current Topics in Medicinal Chemistry. 12: 1363-75. PMID 22690683 DOI: 10.2174/156802612801319016  0.469
2012 Christofferson AJ, Huang N. How to benchmark methods for structure-based virtual screening of large compound libraries. Methods in Molecular Biology (Clifton, N.J.). 819: 187-95. PMID 22183538 DOI: 10.1007/978-1-61779-465-0_13  0.45
2011 Christofferson A, Zhao L, Sun H, Huang Z, Huang N. Theoretical studies of the base pair fidelity of selenium-modified DNA. The Journal of Physical Chemistry. B. 115: 10041-8. PMID 21770426 DOI: 10.1021/Jp204204X  0.402
2011 Pei Q, Christofferson A, Zhang H, Chai J, Huang N. Computational investigation of the enzymatic mechanisms of phosphothreonine lyase. Biophysical Chemistry. 157: 16-23. PMID 21558045 DOI: 10.1016/J.Bpc.2011.04.002  0.308
2010 Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. Plos One. 5: e10109. PMID 20404926 DOI: 10.1371/Journal.Pone.0010109  0.635
2009 Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. Automated docking screens: a feasibility study. Journal of Medicinal Chemistry. 52: 5712-20. PMID 19719084 DOI: 10.1021/Jm9006966  0.726
2009 Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 77: 52-61. PMID 19382204 DOI: 10.1002/Prot.22415  0.635
2008 Huang Z, Feng Y, Chen D, Wu X, Huang S, Wang X, Xiao X, Li W, Huang N, Gu L, Zhong G, Chai J. Structural basis for activation and inhibition of the secreted chlamydia protease CPAF. Cell Host & Microbe. 4: 529-42. PMID 19064254 DOI: 10.1016/J.Chom.2008.10.005  0.309
2008 Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. Journal of Medicinal Chemistry. 51: 4862-5. PMID 18680357 DOI: 10.1021/Jm8006239  0.541
2008 Chen L, Wang H, Zhang J, Gu L, Huang N, Zhou JM, Chai J. Structural basis for the catalytic mechanism of phosphothreonine lyase. Nature Structural & Molecular Biology. 15: 101-2. PMID 18084305 DOI: 10.1038/Nsmb1329  0.323
2007 Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Current Opinion in Drug Discovery & Development. 10: 325-31. PMID 17554859  0.6
2006 Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Physical Chemistry Chemical Physics : Pccp. 8: 5166-77. PMID 17203140 DOI: 10.1039/B608269F  0.642
2006 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. Journal of Medicinal Chemistry. 49: 6789-801. PMID 17154509 DOI: 10.1021/Jm0608356  0.617
2006 Banavali NK, Huang N, MacKerell AD. Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. The Journal of Physical Chemistry. B. 110: 10997-1004. PMID 16771353 DOI: 10.1021/Jp0561322  0.712
2006 Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. Journal of Chemical Information and Modeling. 46: 243-53. PMID 16426060 DOI: 10.1021/Ci0502855  0.655
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 1: 153-68. PMID 26641126 DOI: 10.1021/Ct049930P  0.503
2005 Huang N, MacKerell AD. Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. Journal of Molecular Biology. 345: 265-74. PMID 15571720 DOI: 10.1016/J.Jmb.2004.10.042  0.598
2004 Huang N, MacKerell AD. Atomistic view of base flipping in DNA. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 362: 1439-60. PMID 15306460 DOI: 10.1098/Rsta.2004.1383  0.598
2004 Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Research. 32: 3877-86. PMID 15273274 DOI: 10.1093/Nar/Gkh701  0.721
2004 Huang N, Nagarsekar A, Xia G, Hayashi J, MacKerell AD. Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. Journal of Medicinal Chemistry. 47: 3502-11. PMID 15214778 DOI: 10.1021/Jm030470E  0.577
2003 Peng H, Huang N, Qi J, Xie P, Xu C, Wang J, Yang C. Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening. Bioorganic & Medicinal Chemistry Letters. 13: 3693-9. PMID 14552760 DOI: 10.1016/J.Bmcl.2003.08.014  0.314
2003 Pan Y, Huang N, Cho S, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening Journal of Chemical Information and Computer Sciences. 43: 267-272. PMID 12546562 DOI: 10.1021/Ci020055F  0.565
2003 Huang N, Banavali NK, MacKerell AD. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proceedings of the National Academy of Sciences of the United States of America. 100: 68-73. PMID 12506195 DOI: 10.1073/Pnas.0135427100  0.708
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