| Year |
Citation |
Score |
| 2023 |
Luo Z, Ni F, Wang Q, Ma J. OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Nature Methods. PMID 37813988 DOI: 10.1038/s41592-023-02031-6 |
0.525 |
|
| 2020 |
Xu G, Wang Q, Ma J. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling. Journal of Chemical Theory and Computation. PMID 32324993 DOI: 10.1021/Acs.Jctc.0C00186 |
0.353 |
|
| 2020 |
Xu G, Wang Q, Ma J. OPUS-Refine: A Fast Sampling-based Framework for Refining Protein Backbone Torsion Angles and Global Conformation. Journal of Chemical Theory and Computation. PMID 31935088 DOI: 10.1021/Acs.Jctc.9B01054 |
0.348 |
|
| 2019 |
Xu G, Ma T, Du J, Wang Q, Ma J. OPUS-Rota2: An Improved Fast and Accurate Side-chain Modeling Method. Journal of Chemical Theory and Computation. PMID 31412199 DOI: 10.1021/Acs.Jctc.9B00309 |
0.333 |
|
| 2019 |
Xu G, Ma T, Wang Q, Ma J. OPUS-SSF: A Side-chain-inclusive Scoring Function for Ranking Protein Structural Models. Protein Science : a Publication of the Protein Society. PMID 30919509 DOI: 10.1002/Pro.3608 |
0.351 |
|
| 2019 |
Xie Q, Wang Z, Ni F, Chen X, Ma J, Patel N, Lu H, Liu Y, Tian JH, Flyer D, Massare MJ, Ellingsworth L, Glenn G, Smith G, Wang Q. Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein. Plos One. 14: e0210749. PMID 30730999 DOI: 10.1371/Journal.Pone.0210749 |
0.548 |
|
| 2018 |
Zang T, Ma T, Wang Q, Ma J. Improving low-accuracy protein structures using enhanced sampling techniques. The Journal of Chemical Physics. 149: 072319. PMID 30134714 DOI: 10.1063/1.5027243 |
0.357 |
|
| 2018 |
Ma T, Zang T, Wang Q, Ma J. Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model. Protein Science : a Publication of the Protein Society. PMID 30098055 DOI: 10.1002/Pro.3486 |
0.37 |
|
| 2018 |
Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill. Proceedings of the National Academy of Sciences of the United States of America. PMID 30012616 DOI: 10.1073/Pnas.1805442115 |
0.32 |
|
| 2018 |
Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Research. PMID 29992232 DOI: 10.1093/Nar/Gky595 |
0.736 |
|
| 2017 |
Xu G, Ma T, Zang T, Wang Q, Ma J. OPUS-CSF: A C-atom-based Scoring Function for Ranking Protein Structural Models. Protein Science : a Publication of the Protein Society. PMID 29047165 DOI: 10.1002/Pro.3327 |
0.31 |
|
| 2017 |
Xu G, Ma T, Zang T, Sun W, Wang Q, Ma J. OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing. Journal of Molecular Biology. PMID 28864201 DOI: 10.1016/J.Jmb.2017.08.013 |
0.337 |
|
| 2016 |
Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Lowered pH Leads to Fusion Peptide Release and a Highly-Dynamic Intermediate of Influenza Hemagglutinin. The Journal of Physical Chemistry. B. PMID 27541202 DOI: 10.1021/Acs.Jpcb.6B06775 |
0.315 |
|
| 2016 |
Cai Q, Li DK, Zhou RR, Zhuang SY, Ma JT, Wu YD, Wu AX. Acid-Catalyzed Multicomponent Tandem Double Cyclization: A One-pot, Metal-free Route to Synthesize Polyfunctional 4,9-Dihydropyrrolo[2,1-b]quinazolines. The Journal of Organic Chemistry. PMID 27504693 DOI: 10.1021/acs.joc.6b01660 |
0.396 |
|
| 2016 |
Zhang F, Wu L, Qian J, Qu B, Xia S, La T, Wu Y, Ma J, Zeng J, Guo Q, Cui Y, Yang W, Huang J, Zhu W, Yao Y, et al. Identification of the long noncoding RNA NEAT1 as a novel inflammatory regulator acting through MAPK pathway in human lupus. Journal of Autoimmunity. PMID 27481557 DOI: 10.1016/J.Jaut.2016.07.012 |
0.391 |
|
| 2016 |
Gallego-Perez D, Chang L, Shi J, Ma J, Kim SH, Zhao X, Malkoc V, Wang X, Minata M, Kwak KJ, Wu Y, Lafyatis G, Lu W, Hansford DJ, Nakano I, et al. On-chip clonal analysis of glioma stem cell motility and therapy resistance. Nano Letters. PMID 27420544 DOI: 10.1021/acs.nanolett.6b00902 |
0.413 |
|
| 2016 |
Wu YH, Han ZB, Ma JZ, He Y, Liu LY, Xin SG, Yu Z. [Intermolecular Interactions between Cytisine and Bovine Serum Albumin A Synchronous Fluorescence Spectroscopic Analysis and Molecular Docking Research]. Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. 36: 765-9. PMID 27400521 |
0.426 |
|
| 2016 |
Zheng KL, Shu WM, Ma JR, Wu YD, Wu AX. Acid-Mediated N-H/α,β-C(sp(3))-H Trifunctionalization of Pyrrolidine: Intermolecular [3 + 2] Cycloaddition for the Construction of 2,3-Dihydro-1H-Pyrrolizine Derivatives. Organic Letters. PMID 27396906 DOI: 10.1021/acs.orglett.6b01369 |
0.38 |
|
| 2016 |
Li X, Zhou Z, Ding J, Wu Y, Zhou B, Wang R, Ma J, Wang S, Zhang X, Xia Z, Chen J, Wu J. Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize. Frontiers in Plant Science. 7: 833. PMID 27379126 DOI: 10.3389/fpls.2016.00833 |
0.401 |
|
| 2016 |
Xia L, Wu Y, Ma JI, Yang J, Zhang F. The antibacterial peptide from Bombyx mori cecropinXJ induced growth arrest and apoptosis in human hepatocellular carcinoma cells. Oncology Letters. 12: 57-62. PMID 27347099 DOI: 10.3892/ol.2016.4601 |
0.396 |
|
| 2016 |
Wu Y, Liu J, Ma J, Liu Y, Wang Y, Wu D. Ratiometric nanothermometer based on Rhodamine dye-incorporated F127-melamine-formaldehyde polymer nanoparticle: preparation, characterization, wide-range temperature sensing, and precise intracellular thermometry. Acs Applied Materials & Interfaces. PMID 27197838 DOI: 10.1021/acsami.6b03366 |
0.417 |
|
| 2016 |
Wu YD, Zhou DH, Zhang LX, Zheng WB, Ma JG, Wang M, Zhu XQ, Xu MJ. Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for equipment-free detection of Cryptosporidium spp. oocysts in dairy cattle feces. Parasitology Research. PMID 27174027 DOI: 10.1007/s00436-016-5120-4 |
0.407 |
|
| 2016 |
Wu Y, Zhao X, Chen C, He J, Rong J, Ma J. Modeling the influence of Chevron alignment sign on young male driver performance: A driving simulator study. Accident; Analysis and Prevention. PMID 27161563 DOI: 10.1016/j.aap.2016.04.024 |
0.427 |
|
| 2016 |
Wei L, Ma J, Wang S, Wu Y. Isolation and Functional Characterization of a Novel Gene Encoding a Dehydration Responsive Element Binding Transcription Factor from Populus euphratica. Protein and Peptide Letters. PMID 27001404 |
0.425 |
|
| 2016 |
Wang M, Lü XY, Ma JY, Xiong H, Si LG, Wu Y. Controllable chaos in hybrid electro-optomechanical systems. Scientific Reports. 6: 22705. PMID 26948505 DOI: 10.1038/srep22705 |
0.383 |
|
| 2016 |
Guo R, Ai L, Cao N, Ma J, Wu Y, Wu J, Sun X. Physicochemical properties and structural characterization of a galactomannan from Sophora alopecuroides L. seeds. Carbohydrate Polymers. 140: 451-60. PMID 26876873 DOI: 10.1016/j.carbpol.2015.12.058 |
0.427 |
|
| 2016 |
Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, ... ... Ma J, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 12: 1-222. PMID 26799652 DOI: 10.1080/15548627.2015.1100356 |
0.439 |
|
| 2016 |
Lin X, Noel JK, Eddy NR, Ma J, Onuchic JN. Investigation of the pH Induced Conformational Rearrangement of Influenza Hemagglutinin Biophysical Journal. 110: 13a. DOI: 10.1016/J.Bpj.2015.11.126 |
0.307 |
|
| 2015 |
ZHENG WB, WU YD, MA JG, ZHU XQ, ZHOU DH. [Recombinase Polymerase Amplification and its Applications in Parasite Detection]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi = Chinese Journal of Parasitology & Parasitic Diseases. 33: 382-6. PMID 26931046 |
0.395 |
|
| 2015 |
Wu Y, Wang X, Wang C, Sun Q, Song N, Zhou Y, Jiang Q, Qiao Y, Xu J, Liang L, Tang H, Ma J, Gao X, Chen SD. Prevalence and clinical features of non-motor symptoms of essential tremor in Shanghai rural area. Parkinsonism & Related Disorders. PMID 26777409 DOI: 10.1016/j.parkreldis.2015.10.617 |
0.372 |
|
| 2015 |
Su Y, Ma J, Du L, Xia J, Wu Y, Jia X, Cai Y, Li Y, Zhao J, Liu Q. Application of acoustic radiation force impulse imaging (ARFI) in quantitative evaluation of neonatal brain development. Clinical and Experimental Obstetrics & Gynecology. 42: 797-800. PMID 26753489 |
0.372 |
|
| 2015 |
Wang R, Zhang ZZ, Ma J, Yang Y, Lin P, Wu Y. Spectral properties of the temporal evolution of brain network structure. Chaos (Woodbury, N.Y.). 25: 123112. PMID 26723151 DOI: 10.1063/1.4937451 |
0.398 |
|
| 2015 |
Wu L, Qin Y, Xia S, Dai M, Han X, Wu Y, Zhang X, Ma J, Wang Y, Tang Y, Liu Z, Zhu W, Jallal B, Yao Y, Qu B, et al. Identification of Cyclin-dependent Kinase 1 as a Novel Regulator of Type 1 Interferon Signaling in Systemic Lupus Erythematosus. Arthritis & Rheumatology (Hoboken, N.J.). PMID 26663909 DOI: 10.1002/Art.39543 |
0.388 |
|
| 2015 |
Zhang C, Wang Q, Ma J. Deformable complex network for refining low-resolution X-ray structures. Acta Crystallographica. Section D, Biological Crystallography. 71: 2150-7. PMID 26527134 DOI: 10.1107/S139900471501528X |
0.308 |
|
| 2015 |
Chen X, Ni F, Kondrashkina E, Ma J, Wang Q. Mechanisms of leiomodin 2-mediated regulation of actin filament in muscle cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 26417072 DOI: 10.1073/Pnas.1512464112 |
0.571 |
|
| 2015 |
Yao Y, Wu Y, Wang Y, Verginelli I, Zeng T, Suuberg EM, Jiang L, Wen Y, Ma J. A petroleum vapor intrusion model involving upward advective soil gas flow due to methane generation. Environmental Science & Technology. PMID 26322369 DOI: 10.1021/acs.est.5b01314 |
0.398 |
|
| 2015 |
Song J, Wu Y, Nie F, Wang B, Li Y, Shu A, Ma Y, Zhang R, Kelsoe JR, Ma J. [Analysis of chromosome regions 8q11.1-q13.3, 1q32-q34.3 and 14q31.1-q13.3 in a Chinese family with congenital preauricular fistula]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi = Zhonghua Yixue Yichuanxue Zazhi = Chinese Journal of Medical Genetics. 32: 472-5. PMID 26252087 DOI: 10.3760/cma.j.issn.1003-9406.2015.04.004 |
0.359 |
|
| 2015 |
Lü XY, Jing H, Ma JY, Wu Y. PT-Symmetry-Breaking Chaos in Optomechanics. Physical Review Letters. 114: 253601. PMID 26197125 |
0.401 |
|
| 2015 |
Wu Y, Long Y, Li QL, Han S, Ma J, Yang YW, Gao H. Layer-by-Layer (LBL) Self-Assembled Biohybrid Nanomaterials for Efficient Antibacterial Applications. Acs Applied Materials & Interfaces. PMID 26192024 DOI: 10.1021/Acsami.5B04216 |
0.407 |
|
| 2015 |
Yin L, Wu Y, Gao J, Ma J, Hu Z, Zou G, Zhang Q. Optically binary liquid crystalline blue phases induced by one-armed cholesterol-linked azobenzene molecules. Soft Matter. PMID 26144839 DOI: 10.1039/c5sm01062d |
0.391 |
|
| 2015 |
Zhou C, Wu YL, Chen G, Feng J, Liu XQ, Wang C, Zhang S, Wang J, Zhou S, Ren S, Lu S, Zhang L, Hu C, Hu C, Luo Y, ... ... Ma J, et al. Final overall survival results from a randomised, Phase III study of erlotinib versus chemotherapy as first-line treatment of EGFR mutation-positive advanced non-small-cell lung cancer (OPTIMAL, CTONG-0802). Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. PMID 26141208 DOI: 10.1093/annonc/mdv276 |
0.373 |
|
| 2015 |
Zhang CR, Ma JG, Zhe JW, Jin NZ, Shen YL, Wu YZ, Chen YH, Liu ZJ, Chen HS. The electronic structure engineering of organic dye sensitizers for solar cells: The case of JK derivatives. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 150: 855-866. PMID 26116996 DOI: 10.1016/j.saa.2015.06.060 |
0.428 |
|
| 2015 |
Sun L, Miao Z, Cai C, Zhang D, Zhao M, Wu Y, Zhang X, Swarm SA, Zhou L, Zhang ZJ, Nelson RL, Ma J. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nature Genetics. PMID 26098868 DOI: 10.1038/ng.3339 |
0.409 |
|
| 2015 |
Wu Y, Zhang H, Liu Y, Chen W, Ma J, Li S, Qin Z. Synthesis and Gas Sensing Properties of Single La-Doped SnO2 Nanobelts. Sensors (Basel, Switzerland). 15: 14230-40. PMID 26087374 DOI: 10.3390/s150614230 |
0.397 |
|
| 2015 |
Ma J, You C, Si LG, Xiong H, Li J, Yang X, Wu Y. Optomechanically induced transparency in the presence of an external time-harmonic-driving force. Scientific Reports. 5: 11278. PMID 26062029 DOI: 10.1038/srep11278 |
0.403 |
|
| 2015 |
Jiang QW, Wang C, Zhou Y, Hou MM, Wang X, Tang HD, Wu YW, Ma JF, Chen SD. Plasma epidermal growth factor decreased in the early stage of Parkinson's disease. Aging and Disease. 6: 168-73. PMID 26029474 DOI: 10.14336/AD.2014.0925 |
0.369 |
|
| 2015 |
Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TM, Birck C, Brautigam CA, Brennerman W, Byron O, ... ... Ma J, et al. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. Plos One. 10: e0126420. PMID 25997164 DOI: 10.1371/Journal.Pone.0126420 |
0.438 |
|
| 2015 |
Wu Y, Zhang F, Ma J, Zhang X, Wu L, Qu B, Xia S, Chen S, Tang Y, Shen N. Association of large intergenic noncoding RNA expression with disease activity and organ damage in systemic lupus erythematosus. Arthritis Research & Therapy. 17: 131. PMID 25994030 DOI: 10.1186/s13075-015-0632-3 |
0.394 |
|
| 2015 |
Ma JR, Shu WM, Zheng KL, Ni F, Yin GD, Wu AX. Efficient approach to 2-hydroxy-2,3-dihydrofuran derivatives and its application for the synthesis of novel 4-(1H-pyrazol-4-yl)pyridazines. Organic & Biomolecular Chemistry. 13: 4976-80. PMID 25821120 DOI: 10.1039/c5ob00163c |
0.457 |
|
| 2015 |
He FJ, Wu Y, Feng XX, Ma J, Ma Y, Wang H, Zhang J, Yuan J, Lin CP, Nowson C, MacGregor GA. School based education programme to reduce salt intake in children and their families (School-EduSalt): cluster randomised controlled trial. Bmj (Clinical Research Ed.). 350: h770. PMID 25788018 DOI: 10.1136/Bmj.H770 |
0.375 |
|
| 2015 |
Wu Y, Ma J, Woods PS, Chesarino NM, Liu C, Lee LJ, Nana-Sinkam SP, Davis IC. Selective targeting of alveolar type II respiratory epithelial cells by anti-surfactant protein-C antibody-conjugated lipoplexes. Journal of Controlled Release : Official Journal of the Controlled Release Society. 203: 140-9. PMID 25687308 DOI: 10.1016/j.jconrel.2015.02.016 |
0.402 |
|
| 2015 |
Ma J, Jiang Q, Xu J, Sun Q, Qiao Y, Chen W, Wu Y, Wang Y, Xiao Q, Liu J, Tang H, Chen S. Plasma insulin-like growth factor 1 is associated with cognitive impairment in Parkinson's disease. Dementia and Geriatric Cognitive Disorders. 39: 251-6. PMID 25661865 DOI: 10.1159/000371510 |
0.37 |
|
| 2015 |
Wu Y, Wang L, Ma J, Song Y, Zhang P, Luo A, Fu C, Cao Z, Wang X, Shryock JC, Belardinelli L. Protein kinase C and Ca(2+) -calmodulin-dependent protein kinase II mediate the enlarged reverse INCX induced by ouabain-increased late sodium current in rabbit ventricular myocytes. Experimental Physiology. 100: 399-409. PMID 25641541 DOI: 10.1113/expphysiol.2014.083972 |
0.395 |
|
| 2015 |
Yao Y, Wu Y, Suuberg EM, Provoost J, Shen R, Ma J, Liu J. Vapor intrusion attenuation factors relative to subslab and source, reconsidered in light of background data. Journal of Hazardous Materials. 286: 553-61. PMID 25618001 DOI: 10.1016/j.jhazmat.2015.01.013 |
0.397 |
|
| 2015 |
Zhao X, Ding H, Wu Y, Ma J, Zhong L. Experimental research on safety impacts of the inside shoulder based on driving simulation. Accident; Analysis and Prevention. 76: 6-14. PMID 25557094 DOI: 10.1016/j.aap.2014.12.014 |
0.405 |
|
| 2015 |
Ma J, Zhao D, Wu Y, Xu C, Zhang F. Cyclic stretch induced gene expression of extracellular matrix and adhesion molecules in human periodontal ligament cells. Archives of Oral Biology. 60: 447-55. PMID 25541636 DOI: 10.1016/j.archoralbio.2014.11.019 |
0.394 |
|
| 2014 |
Ma JG, Zhang CR, Gong JJ, Yang B, Zhang HM, Wang W, Wu YZ, Chen YH, Chen HS. The adsorption of α-cyanoacrylic acid on anatase TiO2 (101) and (001) surfaces: a density functional theory study. The Journal of Chemical Physics. 141: 234705. PMID 25527955 DOI: 10.1063/1.4903790 |
0.409 |
|
| 2014 |
Ni F, Yang Y, Shu WM, Ma JR, Wu AX. Brønsted acid promoted addition-cyclization and C-C bond cleavage: a convenient synthesis of 2-amino-5-aroylmethylthiazoles derivatives. Organic & Biomolecular Chemistry. 12: 9466-70. PMID 25327278 DOI: 10.1039/c4ob01519c |
0.47 |
|
| 2014 |
Lin X, Eddy NR, Noel JK, Whitford PC, Wang Q, Ma J, Onuchic JN. Order and disorder control the functional rearrangement of influenza hemagglutinin. Proceedings of the National Academy of Sciences of the United States of America. 111: 12049-54. PMID 25082896 DOI: 10.1073/Pnas.1412849111 |
0.333 |
|
| 2013 |
Chen X, Ni F, Tian X, Kondrashkina E, Wang Q, Ma J. Structural basis of actin filament nucleation by tandem W domains. Cell Reports. 3: 1910-20. PMID 23727244 DOI: 10.1016/J.Celrep.2013.04.028 |
0.549 |
|
| 2013 |
Lu M, Ma J. PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment. Journal of Molecular Biology. 425: 1082-98. PMID 23333742 DOI: 10.1016/J.Jmb.2012.12.026 |
0.326 |
|
| 2012 |
Zhang C, Ma J. Folding helical proteins in explicit solvent using dihedral-biased tempering. Proceedings of the National Academy of Sciences of the United States of America. 109: 8139-44. PMID 22573819 DOI: 10.1073/Pnas.1112143109 |
0.319 |
|
| 2012 |
Lu M, Ming D, Ma J. fSUB: normal mode analysis with flexible substructures. The Journal of Physical Chemistry. B. 116: 8636-45. PMID 22448847 DOI: 10.1021/Jp300312U |
0.33 |
|
| 2012 |
Zeng J, Kirk BD, Gou Y, Wang Q, Ma J. Genome-wide polycomb target gene prediction in Drosophila melanogaster. Nucleic Acids Research. 40: 5848-63. PMID 22416065 DOI: 10.1093/Nar/Gks209 |
0.747 |
|
| 2011 |
Xu J, Liu S, Chen M, Ma J, Matthews KS. Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor. Biochemistry. 50: 9002-13. PMID 21928765 DOI: 10.1021/Bi200896T |
0.312 |
|
| 2011 |
Lu M, Ma J. Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models. Archives of Biochemistry and Biophysics. 508: 64-71. PMID 21211510 DOI: 10.1016/J.Abb.2010.12.031 |
0.349 |
|
| 2010 |
Zhang C, Ma J. Enhanced sampling and applications in protein folding in explicit solvent. The Journal of Chemical Physics. 132: 244101. PMID 20590175 DOI: 10.1063/1.3435332 |
0.334 |
|
| 2010 |
Chen X, Wang Q, Ni F, Ma J. Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement. Proceedings of the National Academy of Sciences of the United States of America. 107: 11352-7. PMID 20534430 DOI: 10.1073/Pnas.1000142107 |
0.595 |
|
| 2009 |
Ni F, Poon BK, Wang Q, Ma J. Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit. Acta Crystallographica. Section D, Biological Crystallography. 65: 633-43. PMID 19564683 DOI: 10.1107/S0907444909010695 |
0.764 |
|
| 2009 |
Ma J. Explicit orientation dependence in empirical potentials and its significance to side-chain modeling. Accounts of Chemical Research. 42: 1087-96. PMID 19445451 DOI: 10.1021/Ar900009E |
0.364 |
|
| 2009 |
Chen X, Lu M, Poon BK, Wang Q, Ma J. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement. Acta Crystallographica. Section D, Biological Crystallography. 65: 339-47. PMID 19307715 DOI: 10.1107/S0907444909003539 |
0.725 |
|
| 2009 |
Weng J, Ma J, Fan K, Wang W. Asymmetric conformational flexibility in the ATP-binding cassette transporter HI1470/1. Biophysical Journal. 96: 1918-30. PMID 19254551 DOI: 10.1016/J.Bpj.2008.11.035 |
0.301 |
|
| 2009 |
Chen M, Dousis AD, Wu Y, Wittung-Stafshede P, Ma J. Predicting protein folding cores by empirical potential functions. Archives of Biochemistry and Biophysics. 483: 16-22. PMID 19135974 DOI: 10.1016/J.Abb.2008.12.011 |
0.773 |
|
| 2009 |
Shen J, Kirk BD, Ma J, Wang Q. Diversifying selective pressure on influenza B virus hemagglutinin. Journal of Medical Virology. 81: 114-24. PMID 19031453 DOI: 10.1002/Jmv.21335 |
0.739 |
|
| 2009 |
Wu Y, Dousis AD, Chen M, Li J, Ma J. OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries. Journal of Molecular Biology. 385: 1314-29. PMID 19026662 DOI: 10.1016/J.Jmb.2008.10.093 |
0.765 |
|
| 2008 |
Lu M, Ma J. A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proceedings of the National Academy of Sciences of the United States of America. 105: 15358-63. PMID 18832168 DOI: 10.1073/Pnas.0806072105 |
0.349 |
|
| 2008 |
Lu M, Dousis AD, Ma J. OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Science : a Publication of the Protein Society. 17: 1576-85. PMID 18556476 DOI: 10.1110/Ps.035022.108 |
0.764 |
|
| 2008 |
Lu M, Dousis AD, Ma J. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. Journal of Molecular Biology. 376: 288-301. PMID 18177896 DOI: 10.1016/J.Jmb.2007.11.033 |
0.782 |
|
| 2008 |
Cheng F, Wang Q, Chen M, Quiocho FA, Ma J. Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands. Proteins. 70: 1228-34. PMID 17847090 DOI: 10.1002/Prot.21615 |
0.321 |
|
| 2007 |
Chen X, Poon BK, Dousis A, Wang Q, Ma J. Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution. Structure (London, England : 1993). 15: 955-62. PMID 17698000 DOI: 10.1016/J.Str.2007.06.012 |
0.771 |
|
| 2007 |
Wu Y, Lu M, Chen M, Li J, Ma J. OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Science : a Publication of the Protein Society. 16: 1449-63. PMID 17586777 DOI: 10.1110/Ps.072796107 |
0.501 |
|
| 2007 |
Poon BK, Chen X, Lu M, Vyas NK, Quiocho FA, Wang Q, Ma J. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution. Proceedings of the National Academy of Sciences of the United States of America. 104: 7869-74. PMID 17470791 DOI: 10.1073/Pnas.0701204104 |
0.711 |
|
| 2006 |
Lu M, Poon B, Ma J. A New Method for Coarse-Grained Elastic Normal-Mode Analysis. Journal of Chemical Theory and Computation. 2: 464-471. PMID 21760758 DOI: 10.1021/Ct050307U |
0.702 |
|
| 2006 |
Chen M, Wilson CJ, Wu Y, Wittung-Stafshede P, Ma J. Correlation between protein stability cores and protein folding kinetics: a case study on Pseudomonas aeruginosa apo-azurin. Structure (London, England : 1993). 14: 1401-10. PMID 16962971 DOI: 10.1016/J.Str.2006.07.007 |
0.542 |
|
| 2006 |
Kong Y, Ma J, Karplus M, Lipscomb WN. The allosteric mechanism of yeast chorismate mutase: a dynamic analysis. Journal of Molecular Biology. 356: 237-47. PMID 16337651 DOI: 10.1016/J.Jmb.2005.10.064 |
0.327 |
|
| 2005 |
Perham M, Chen M, Ma J, Wittung-Stafshede P. Unfolding of heptameric co-chaperonin protein follows "fly casting" mechanism: observation of transient nonnative heptamer. Journal of the American Chemical Society. 127: 16402-3. PMID 16305220 DOI: 10.1021/Ja055574O |
0.32 |
|
| 2005 |
Wu Y, Tian X, Lu M, Chen M, Wang Q, Ma J. Folding of small helical proteins assisted by small-angle X-ray scattering profiles. Structure (London, England : 1993). 13: 1587-97. PMID 16271882 DOI: 10.1016/J.Str.2005.07.023 |
0.556 |
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| 2005 |
Lu M, Ma J. The role of shape in determining molecular motions. Biophysical Journal. 89: 2395-401. PMID 16055547 DOI: 10.1529/Biophysj.105.065904 |
0.301 |
|
| 2005 |
Wu Y, Chen M, Lu M, Wang Q, Ma J. Determining protein topology from skeletons of secondary structures. Journal of Molecular Biology. 350: 571-86. PMID 15961102 DOI: 10.1016/J.Jmb.2005.04.064 |
0.565 |
|
| 2005 |
Muralidhara BK, Chen M, Ma J, Wittung-Stafshede P. Effect of inorganic phosphate on FMN binding and loop flexibility in Desulfovibrio desulfuricans apo-flavodoxin. Journal of Molecular Biology. 349: 87-97. PMID 15876370 DOI: 10.1016/J.Jmb.2005.03.054 |
0.312 |
|
| 2005 |
Trakhanov S, Vyas NK, Luecke H, Kristensen DM, Ma J, Quiocho FA. Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Biochemistry. 44: 6597-608. PMID 15850393 DOI: 10.1021/Bi047302O |
0.332 |
|
| 2005 |
Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure (London, England : 1993). 13: 373-80. PMID 15766538 DOI: 10.1016/J.Str.2005.02.002 |
0.321 |
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| 2005 |
Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496 |
0.303 |
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| 2004 |
van der Vaart A, Ma J, Karplus M. The unfolding action of GroEL on a protein substrate. Biophysical Journal. 87: 562-73. PMID 15240489 DOI: 10.1529/Biophysj.103.037333 |
0.32 |
|
| 2004 |
Kong Y, Zhang X, Baker TS, Ma J. A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. Journal of Molecular Biology. 339: 117-30. PMID 15123425 DOI: 10.1016/J.Jmb.2004.03.038 |
0.302 |
|
| 2004 |
Flynn TC, Ma J. Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament. Biophysical Journal. 86: 3204-10. PMID 15111433 DOI: 10.1016/S0006-3495(04)74368-4 |
0.56 |
|
| 2004 |
Ma J. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Current Protein & Peptide Science. 5: 119-23. PMID 15078222 DOI: 10.2174/1389203043486892 |
0.349 |
|
| 2004 |
Brink J, Ludtke SJ, Kong Y, Wakil SJ, Ma J, Chiu W. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (London, England : 1993). 12: 185-91. PMID 14962379 DOI: 10.1016/J.Str.2004.01.015 |
0.358 |
|
| 2004 |
Wu Y, Ma J. Refinement of F-actin model against fiber diffraction data by long-range normal modes. Biophysical Journal. 86: 116-24. PMID 14695255 DOI: 10.1016/S0006-3495(04)74089-8 |
0.526 |
|
| 2003 |
Huyton T, Pye VE, Briggs LC, Flynn TC, Beuron F, Kondo H, Ma J, Zhang X, Freemont PS. The crystal structure of murine p97/VCP at 3.6A. Journal of Structural Biology. 144: 337-48. PMID 14643202 DOI: 10.1016/J.Jsb.2003.10.007 |
0.579 |
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| 2003 |
Flynn TC, Swint-Kruse L, Kong Y, Booth C, Matthews KS, Ma J. Allosteric transition pathways in the lactose repressor protein core domains: asymmetric motions in a homodimer. Protein Science : a Publication of the Protein Society. 12: 2523-41. PMID 14573864 DOI: 10.1110/Ps.03188303 |
0.589 |
|
| 2003 |
Kong Y, Ma J. A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps. Journal of Molecular Biology. 332: 399-413. PMID 12948490 DOI: 10.1016/S0022-2836(03)00859-3 |
0.314 |
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| 2003 |
Ming D, Kong Y, Wu Y, Ma J. Simulation of F-actin filaments of several microns. Biophysical Journal. 85: 27-35. PMID 12829461 DOI: 10.1016/S0006-3495(03)74451-8 |
0.517 |
|
| 2003 |
Kong Y, Ming D, Wu Y, Stoops JK, Zhou ZH, Ma J. Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. Journal of Molecular Biology. 330: 129-35. PMID 12818207 DOI: 10.1016/S0022-2836(03)00555-2 |
0.543 |
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| 2003 |
Beuron F, Flynn TC, Ma J, Kondo H, Zhang X, Freemont PS. Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model. Journal of Molecular Biology. 327: 619-29. PMID 12634057 DOI: 10.1016/S0022-2836(03)00178-5 |
0.569 |
|
| 2003 |
Ming D, Kong Y, Wu Y, Ma J. Substructure synthesis method for simulating large molecular complexes. Proceedings of the National Academy of Sciences of the United States of America. 100: 104-9. PMID 12518058 DOI: 10.1073/Pnas.232588999 |
0.55 |
|
| 2002 |
O'Connell MJ, Bachilo SM, Huffman CB, Moore VC, Strano MS, Haroz EH, Rialon KL, Boul PJ, Noon WH, Kittrell C, Ma J, Hauge RH, Weisman RB, Smalley RE. Band gap fluorescence from individual single-walled carbon nanotubes. Science (New York, N.Y.). 297: 593-6. PMID 12142535 DOI: 10.1126/Science.1072631 |
0.718 |
|
| 2002 |
Ma J, Flynn TC, Cui Q, Leslie AG, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure (London, England : 1993). 10: 921-31. PMID 12121647 DOI: 10.1016/S0969-2126(02)00789-X |
0.552 |
|
| 2002 |
Ming D, Kong Y, Lambert MA, Huang Z, Ma J. How to describe protein motion without amino acid sequence and atomic coordinates. Proceedings of the National Academy of Sciences of the United States of America. 99: 8620-5. PMID 12084922 DOI: 10.1073/Pnas.082148899 |
0.384 |
|
| 2002 |
Ming D, Kong Y, Wakil SJ, Brink J, Ma J. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proceedings of the National Academy of Sciences of the United States of America. 99: 7895-9. PMID 12060737 DOI: 10.1073/Pnas.112222299 |
0.372 |
|
| 2002 |
Noon WH, Kong Y, Ma J. Molecular dynamics analysis of a buckyball-antibody complex. Proceedings of the National Academy of Sciences of the United States of America. 99: 6466-70. PMID 11880600 DOI: 10.1073/Pnas.022532599 |
0.744 |
|
| 2000 |
Ma J, Sigler PB, Xu Z, Karplus M. A dynamic model for the allosteric mechanism of GroEL. Journal of Molecular Biology. 302: 303-13. PMID 10970735 DOI: 10.1006/Jmbi.2000.4014 |
0.321 |
|
| 1998 |
Ma J, Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proceedings of the National Academy of Sciences of the United States of America. 95: 8502-7. PMID 9671707 DOI: 10.1073/Pnas.95.15.8502 |
0.373 |
|
| 1998 |
Ma J, Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. Journal of Molecular Biology. 274: 114-31. PMID 9398520 DOI: 10.1006/Jmbi.1997.1313 |
0.348 |
|
| 1997 |
Ma J, Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proceedings of the National Academy of Sciences of the United States of America. 94: 11905-10. PMID 9342335 DOI: 10.1073/Pnas.94.22.11905 |
0.315 |
|
| 1997 |
Ma J, Huo S, Straub JE. Molecular dynamics simulation study of the B-states of solvated carbon monoxymyoglobin Journal of the American Chemical Society. 119: 2541-2551. DOI: 10.1021/Ja9608252 |
0.326 |
|
| 1989 |
Cheng Z, Lou X, Ma J, Shao J, Chen N. Bond‐orientational order in molten salt: Molecular dynamic simulation Journal of Chemical Physics. 91: 4278-4284. DOI: 10.1063/1.456808 |
0.305 |
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