Jianpeng Ma - Publications

Rice University, Houston, TX 
General Biophysics, Biomedical Engineering, Biochemistry

118 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
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  0.76
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  0.76
2019 Wang Y, Ma A, Liu G, Ma J, Wei J, Zhou H, Brandt KK, Zhuang G. Potential feedback mediated by soil microbiome response to warming in a glacier forefield. Global Change Biology. PMID 31782204 DOI: 10.1111/gcb.14936  0.6
2019 Jiang Y, Ma J, Gong T, Hao H, Chen H. The diffuse involvement of anti-N-methyl-D-aspartate receptor encephalitis in brain: a case report. Bmc Neurology. 19: 230. PMID 31558152 DOI: 10.1186/s12883-019-1456-6  0.64
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  0.76
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  0.76
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  0.76
2018 Liu T, Ma J, Cao H, Hou D, Xu L. Evaluation of the diagnostic performance of the simple method of computed tomography in the assessment of patients with shoulder instability: a prospective cohort study. Bmc Medical Imaging. 18: 45. PMID 30470257 DOI: 10.1186/s12880-018-0290-4  0.52
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  0.76
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  0.76
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  0.76
2017 Zhang C, Drake JA, Ma J, Pettitt BM. Optimal updating magnitude in adaptive flat-distribution sampling. The Journal of Chemical Physics. 147: 174105. PMID 29117700 DOI: 10.1063/1.5008618  0.4
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  0.76
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  0.76
2017 Yu L, Lu M, Jia D, Ma J, Ben-Jacob E, Levine H, Kaipparettu BA, Onuchic JN. Modeling the Genetic Regulation of Cancer Metabolism: Interplay Between Glycolysis and Oxidative Phosphorylation. Cancer Research. PMID 28202516 DOI: 10.1158/0008-5472.CAN-16-2074  0.56
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  0.76
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  0.68
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  0.56
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  0.68
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  0.76
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  0.56
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  0.68
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  0.76
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  0.68
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  0.76
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  0.4
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  0.68
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  0.68
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  0.68
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  0.76
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  0.36
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  0.76
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  0.76
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  0.52
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  0.68
2015 Lü XY, Jing H, Ma JY, Wu Y. PT-Symmetry-Breaking Chaos in Optomechanics. Physical Review Letters. 114: 253601. PMID 26197125  0.68
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  0.68
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  0.68
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  0.68
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  0.6
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  0.76
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  0.68
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  0.68
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  0.4
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  0.48
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  0.68
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  0.52
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  0.4
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  0.68
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  0.68
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  0.4
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  0.68
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  0.68
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  0.6
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  0.68
2014 Zang T, Yu L, Zhang C, Ma J. Parallel continuous simulated tempering and its applications in large-scale molecular simulations. The Journal of Chemical Physics. 141: 044113. PMID 25084887 DOI: 10.1063/1.4890038  0.88
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  0.88
2014 Ma J, Liu C, Zhong X, Wang L, Chen X. Emotional body-word conflict evokes enhanced n450 and slow potential. Plos One. 9: e95198. PMID 24819150 DOI: 10.1371/journal.pone.0095198  0.6
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  0.76
2013 Bai F, Xu Y, Chen J, Liu Q, Gu J, Wang X, Ma J, Li H, Onuchic JN, Jiang H. Free energy landscape for the binding process of Huperzine A to acetylcholinesterase. Proceedings of the National Academy of Sciences of the United States of America. 110: 4273-8. PMID 23440190 DOI: 10.1073/pnas.1301814110  0.88
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  0.56
2012 Zhang C, Ma J. Estimating statistical distributions using an integral identity. The Journal of Chemical Physics. 136: 204113. PMID 22667546 DOI: 10.1063/1.4721638  0.4
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  0.4
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  0.56
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  0.88
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  0.88
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  0.56
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  0.4
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  0.76
2009 Shen J, Ma J, Wang Q. Evolutionary trends of A(H1N1) influenza virus hemagglutinin since 1918. Plos One. 4: e7789. PMID 19924230 DOI: 10.1371/journal.pone.0007789  0.76
2009 Yu K, Luo C, Qin G, Xu Z, Li N, Liu H, Shen X, Ma J, Wang Q, Yang C, Zhu W, Jiang H. Why are oseltamivir and zanamivir effective against the newly emerged influenza A virus (A/H1N1)? Cell Research. 19: 1221-4. PMID 19770846 DOI: 10.1038/cr.2009.111  0.76
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  0.88
2009 Zhang C, Ma J. Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk. The Journal of Chemical Physics. 130: 194112. PMID 19466826 DOI: 10.1063/1.3139192  0.4
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  0.88
2009 Zhang C, Ma J. Counting solutions for the N -queens and Latin-square problems by Monte Carlo simulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 016703. PMID 19257162 DOI: 10.1103/PhysRevE.79.016703  0.4
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  0.56
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  0.88
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  0.88
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  0.88
2008 Zhang C, Ma J. Comparison of sampling efficiency between simulated tempering and replica exchange. The Journal of Chemical Physics. 129: 134112. PMID 19045083 DOI: 10.1063/1.2988339  0.4
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  0.56
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  0.88
2008 Wang Q, Cheng F, Lu M, Tian X, Ma J. Crystal structure of unliganded influenza B virus hemagglutinin. Journal of Virology. 82: 3011-20. PMID 18184701 DOI: 10.1128/JVI.02477-07  0.76
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  0.88
2008 Song C, Wen W, Rayala SK, Chen M, Ma J, Zhang M, Kumar R. Serine 88 phosphorylation of the 8-kDa dynein light chain 1 is a molecular switch for its dimerization status and functions. The Journal of Biological Chemistry. 283: 4004-13. PMID 18084006 DOI: 10.1074/jbc.M704512200  0.36
2008 Weng J, Ma J, Fan K, Wang W. The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD. Biophysical Journal. 94: 612-21. PMID 17951296 DOI: 10.1529/biophysj.107.110734  0.56
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  0.88
2007 Fernández A, Sanguino A, Peng Z, Ozturk E, Chen J, Crespo A, Wulf S, Shavrin A, Qin C, Ma J, Trent J, Lin Y, Han HD, Mangala LS, Bankson JA, et al. An anticancer C-Kit kinase inhibitor is reengineered to make it more active and less cardiotoxic. The Journal of Clinical Investigation. 117: 4044-54. PMID 18060038 DOI: 10.1172/JCI32373  0.88
2007 Wang Q, Tian X, Chen X, Ma J. Structural basis for receptor specificity of influenza B virus hemagglutinin. Proceedings of the National Academy of Sciences of the United States of America. 104: 16874-9. PMID 17942670 DOI: 10.1073/pnas.0708363104  0.76
2007 Zhang C, Ma J. Simulation via direct computation of partition functions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 036708. PMID 17930362 DOI: 10.1103/PhysRevE.76.036708  0.4
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  0.88
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  0.68
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  0.88
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  0.56
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  0.88
2006 Singh RR, Kaluarachchi K, Chen M, Rayala SK, Balasenthil S, Ma J, Kumar R. Solution structure and antiestrogenic activity of the unique C-terminal, NR-box motif-containing region of MTA1s. The Journal of Biological Chemistry. 281: 25612-21. PMID 16807247 DOI: 10.1074/jbc.M604444200  0.36
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  0.88
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  0.76
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  0.56
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  0.76
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  0.36
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  0.88
2005 Xu Y, Shen J, Luo X, Zhu W, Chen K, Ma J, Jiang H. Conformational transition of amyloid beta-peptide. Proceedings of the National Academy of Sciences of the United States of America. 102: 5403-7. PMID 15800039 DOI: 10.1073/pnas.0501218102  0.4
2004 Cui Q, Li G, Ma J, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. Journal of Molecular Biology. 340: 345-72. PMID 15201057 DOI: 10.1016/j.jmb.2004.04.044  0.88
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  0.88
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  0.88
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  0.88
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  0.68
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  0.88
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  0.88
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  0.88
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  0.68
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  0.68
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  0.88
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  0.68
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  0.88
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  0.88
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  0.88
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