Research Output

2012

Drug-likeness analysis of traditional chinese medicines: Prediction of drug-likeness using machine learning approaches

Tian, S., Wang, J., Li, Y., Xu, X. & Hou, T., Dec 3 2012, In : Molecular Pharmaceutics. 9, 10, p. 2875-2886 12 p.

Research output: Contribution to journalArticle

57 Scopus citations
30 Scopus citations

Enlightening molecular mechanisms through study of protein interactions

Rizo-Rey, J., Rosen, M. K. & Gardner, K. H., Oct 1 2012, In : Journal of molecular cell biology. 4, 5, p. 270-283 14 p.

Research output: Contribution to journalReview article

16 Scopus citations

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

Toprak, E., Veres, A., Michel, J. B., Chait, R., Hartl, D. L. & Kishony, R., Jan 1 2012, In : Nature genetics. 44, 1, p. 101-105 5 p.

Research output: Contribution to journalArticle

366 Scopus citations

Hydrophobic forces and the length limit of foldable protein domains

Lin, M. M. & Zewail, A. H., Jun 19 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 25, p. 9851-9856 6 p.

Research output: Contribution to journalArticle

20 Scopus citations

Insulin stimulation of SREBP-1c processing in transgenic rat hepatocytes requires p70 S6-kinase

Owen, J. L., Zhang, Y., Bae, S. H., Farooqi, M. S., Liang, G., Hammer, R. E., Goldstein, J. L. & Brown, M. S., Oct 2 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 40, p. 16184-16189 6 p.

Research output: Contribution to journalArticle

137 Scopus citations

In support of the BMRB.

Markley, J. L., Akutsu, H., Asakura, T., Baldus, M., Boelens, R., Bonvin, A., Kaptein, R., Bax, A., Bezsonova, I., Gryk, M. R., Hoch, J. C., Korzhnev, D. M., Maciejewski, M. W., Case, D., Chazin, W. J., Cross, T. A., Dames, S., Kessler, H., Lange, O., Madl, T. & 71 others, Reif, B., Sattler, M., Eliezer, D., Fersht, A., Forman-Kay, J., Kay, L. E., Fraser, J., Gross, J., Kortemme, T., Sali, A., Fujiwara, T., Gardner, K. H., Luo, X., Rizo-Rey, J., Rosen, M. K., Gil, R. R., Ho, C., Rule, G., Gronenborn, A. M., Ishima, R., Klein-Seetharaman, J., Tang, P., van der Wel, P., Xu, Y., Grzesiek, S., Hiller, S., Seelig, J., Laue, E. D., Mott, H., Nietlispach, D., Barsukov, I., Lian, L. Y., Middleton, D., Blumenschein, T., Moore, G., Campbell, I., Schnell, J., Vakonakis, I. J., Watts, A., Conte, M. R., Mason, J., Pfuhl, M., Sanderson, M. R., Craven, J., Williamson, M., Dominguez, C., Roberts, G., Günther, U., Overduin, M., Werner, J., Williamson, P., Blindauer, C., Crump, M., Driscoll, P., Frenkiel, T., Golovanov, A., Matthews, S., Parkinson, J., Uhrin, D., Williams, M., Neuhaus, D., Oschkinat, H., Ramos, A., Shaw, D. E., Steinbeck, C., Vendruscolo, M., Vuister, G. W., Walters, K. J., Weinstein, H., Wüthrich, K. & Yokoyama, S., Sep 2012, In : Nature structural & molecular biology. 19, 9, p. 854-860 7 p.

Research output: Contribution to journalArticle

5 Scopus citations

Modeling cell-to-cell stochastic variability in intrinsic apoptosis pathway

Ooi, H. K. & Ma, L., Dec 14 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. p. 5498-5501 4 p. 6347239. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multiple repeat elements within the FAM21 tail link the WASH actin regulatory complex to the retromer

Jia, D., Gomez, T. S., Billadeau, D. D. & Rosen, M. K., Jun 15 2012, In : Molecular biology of the cell. 23, 12, p. 2352-2361 10 p.

Research output: Contribution to journalArticle

90 Scopus citations

Phase transitions in the assembly of multivalent signalling proteins

Li, P., Banjade, S., Cheng, H. C., Kim, S., Chen, B., Guo, L., Llaguno, M., Hollingsworth, J. V., King, D. S., Banani, S. F., Russo, P. S., Jiang, Q. X., Nixon, B. T. & Rosen, M. K., Mar 15 2012, In : Nature. 483, 7389, p. 336-340 5 p.

Research output: Contribution to journalArticle

662 Scopus citations

Protein folding - Simplicity in complexity

Lin, M. M. & Zewail, A. H., Aug 1 2012, In : Annalen der Physik. 524, 8, p. 379-391 13 p.

Research output: Contribution to journalArticle

15 Scopus citations

Quantifying the rhythm of KaiB-C interaction for in vitro cyanobacterial circadian clock

Ma, L. & Ranganathan, R., Aug 10 2012, In : PloS one. 7, 8, e42581.

Research output: Contribution to journalArticle

11 Scopus citations

Self-organized cell motility from motor-filament interactions

Du, X., Doubrovinski, K. & Osterfield, M., Apr 18 2012, In : Biophysical journal. 102, 8, p. 1738-1745 8 p.

Research output: Contribution to journalArticle

18 Scopus citations

The spatial architecture of protein function and adaptation

McLaughlin, R. N., Poelwijk, F. J., Raman, A., Gosal, W. S. & Ranganathan, R., Nov 1 2012, In : Nature. 491, 7422, p. 138-142 5 p.

Research output: Contribution to journalArticle

233 Scopus citations
2011

Ab initio studies of cellulose I: Crystal structure, intermolecular forces, and interactions with water

Li, Y., Lin, M. & Davenport, J. W., Jun 16 2011, In : Journal of Physical Chemistry C. 115, 23, p. 11533-11539 7 p.

Research output: Contribution to journalArticle

52 Scopus citations

ADME evaluation in drug discovery. 9. Prediction of oral bioavailability in humans based on molecular properties and structural fingerprints

Tian, S., Li, Y., Wang, J., Zhang, J. & Hou, T., Jun 6 2011, In : Molecular Pharmaceutics. 8, 3, p. 841-851 11 p.

Research output: Contribution to journalArticle

55 Scopus citations
60 Scopus citations

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

Wang, J. & Hou, T., Dec 1 2011, In : Journal of Computational Chemistry. 32, 16, p. 3505-3519 15 p.

Research output: Contribution to journalArticle

62 Scopus citations

Arp2/3 complex is bound and activated by two WASP proteins

Padrick, S. B., Doolittle, L. K., Brautigam, C. A., King, D. S. & Rosen, M. K., Aug 16 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 33, p. E472-E479

Research output: Contribution to journalArticle

112 Scopus citations
1038 Scopus citations
403 Scopus citations

Cell motility resulting from spontaneous polymerization waves

Doubrovinski, K. & Kruse, K., Dec 16 2011, In : Physical Review Letters. 107, 25, 258103.

Research output: Contribution to journalArticle

55 Scopus citations

Development of polarizable models for molecular mechanical calculations I: Parameterization of atomic polarizability

Wang, J., Cieplak, P., Li, J., Hou, T., Luo, R. & Duan, Y., Mar 31 2011, In : Journal of Physical Chemistry B. 115, 12, p. 3091-3099 9 p.

Research output: Contribution to journalArticle

89 Scopus citations

Development of polarizable models for molecular mechanical calculations II: Induced dipole models significantly improve accuracy of intermolecular interaction energies

Wang, J., Cieplak, P., Li, J., Wang, J., Cai, Q., Hsieh, M., Lei, H., Luo, R. & Duan, Y., Mar 31 2011, In : Journal of Physical Chemistry B. 115, 12, p. 3100-3111 12 p.

Research output: Contribution to journalArticle

90 Scopus citations

Distinct Interactions Select and Maintain a Specific Cell Fate

Doncic, A., Falleur-Fettig, M. & Skotheim, J. M., Aug 19 2011, In : Molecular cell. 43, 4, p. 528-539 12 p.

Research output: Contribution to journalArticle

81 Scopus citations

qand phospholipase C-β: Turn on, turn off, and do it fast

Ross, E. M., Feb 8 2011, In : Science Signaling. 4, 159, pe5.

Research output: Contribution to journalReview article

18 Scopus citations

Hot spots for allosteric regulation on protein surfaces

Reynolds, K. A., McLaughlin, R. N. & Ranganathan, R., Dec 23 2011, In : Cell. 147, 7, p. 1564-1575 12 p.

Research output: Contribution to journalArticle

177 Scopus citations

Kernel mechanism of the cyanobacterial circadian clock is a relaxation oscillator

Ma, L. & Ranganathan, R., Dec 1 2011, 2011 50th IEEE Conference on Decision and Control and European Control Conference, CDC-ECC 2011. p. 5850-5855 6 p. 6161040. (Proceedings of the IEEE Conference on Decision and Control).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function

Holmstrom, S. R., Deering, T., Swift, G. H., Poelwijk, F. J., Mangelsdorf, D. J., Kliewer, S. A. & Macdonald, R. J., Aug 15 2011, In : Genes and Development. 25, 16, p. 1674-1679 6 p.

Research output: Contribution to journalArticle

65 Scopus citations

Mechanism of actin filament nucleation by the bacterial effector VopL

Yu, B., Cheng, H. C., Brautigam, C. A., Tomchick, D. R. & Rosen, M. K., Sep 1 2011, In : Nature Structural and Molecular Biology. 18, 9, p. 1068-1074 7 p.

Research output: Contribution to journalArticle

42 Scopus citations

Optimality and evolution of transcriptionally regulated gene expression

Poelwijk, F. J., Heyning, P. D., de Vos, M. G. J., Kiviet, D. J. & Tans, S. J., Aug 16 2011, In : BMC Systems Biology. 5, 128.

Research output: Contribution to journalArticle

19 Scopus citations

Recent advances on aqueous solubility prediction

Wang, J. & Hou, T., Jun 1 2011, In : Combinatorial Chemistry and High Throughput Screening. 14, 5, p. 328-338 11 p.

Research output: Contribution to journalArticle

67 Scopus citations

Recent developments of in silico predictions of oral bioavailability

Zhu, J., Wang, J., Yu, H., Li, Y. & Hou, T., Jun 1 2011, In : Combinatorial Chemistry and High Throughput Screening. 14, 5, p. 362-374 13 p.

Research output: Contribution to journalArticle

28 Scopus citations

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

Poelwijk, F. J., Tǎnase-Nicola, S., Kiviet, D. J. & Tans, S. J., Mar 7 2011, In : Journal of Theoretical Biology. 272, 1, p. 141-144 4 p.

Research output: Contribution to journalArticle

102 Scopus citations

Specificity and cooperativity at β-lactamase position 104 in TEM-1/BLIP and SHV-1/BLIP interactions

Hanes, M. S., Reynolds, K. A., Mcnamara, C., Ghosh, P., Bonomo, R. A., Kirsch, J. F. & Handel, T. M., Apr 1 2011, In : Proteins: Structure, Function and Bioinformatics. 79, 4, p. 1267-1276 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Speed limit of protein folding evidenced in secondary structure dynamics

Lin, M. M., Mohammed, O. F., Jas, G. S. & Zewail, A. H., Oct 4 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 40, p. 16622-16627 6 p.

Research output: Contribution to journalArticle

32 Scopus citations

Structural dynamics of free proteins in diffraction

Lin, M. M., Shorokhov, D. & Zewail, A. H., Oct 26 2011, In : Journal of the American Chemical Society. 133, 42, p. 17072-17086 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

Synergistic Ca2+ responses by Gαi- and Gαq-coupled G-protein-coupled receptors require a single PLCβ isoform that is sensitive to both Gβγ and Gαq

Rebres, R. A., Roach, T. I. A., Fraser, I. D. C., Philip, F., Moon, C., Lin, K. M., Liu, J., Santat, L., Cheadle, L., Ross, E. M., Simon, M. I. & Seaman, W. E., Jan 14 2011, In : Journal of Biological Chemistry. 286, 2, p. 942-951 10 p.

Research output: Contribution to journalArticle

31 Scopus citations

The feasibility of parameterizing four-state equilibria using relaxation dispersion measurements

Li, P., Martins, I. R. S. & Rosen, M. K., Sep 1 2011, In : Journal of Biomolecular NMR. 51, 1-2, p. 57-70 14 p.

Research output: Contribution to journalArticle

13 Scopus citations

The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem cells

Gao, Z., Ure, K., Ding, P., Nashaat, M., Yuan, L., Ma, J., Hammer, R. E. & Hsieh, J., Jun 29 2011, In : Journal of Neuroscience. 31, 26, p. 9772-9786 15 p.

Research output: Contribution to journalArticle

156 Scopus citations

The structure of the NPC1L1 N-terminal domain in a closed conformation

Kwon, H. J., Palnitkar, M. & Deisenhofer, J., Apr 25 2011, In : PloS one. 6, 4, e18722.

Research output: Contribution to journalArticle

35 Scopus citations

Tradeoffs and optimality in the evolution of gene regulation

Poelwijk, F. J., De Vos, M. G. J. & Tans, S. J., Aug 5 2011, In : Cell. 146, 3, p. 462-470 9 p.

Research output: Contribution to journalArticle

67 Scopus citations

WNK1 promotes PIP2 synthesis to coordinate growth factor and GPCR-Gq signaling

An, S. W., Cha, S. K., Yoon, J., Chang, S., Ross, E. M. & Huang, C. L., Dec 6 2011, In : Current Biology. 21, 23, p. 1979-1987 9 p.

Research output: Contribution to journalArticle

22 Scopus citations
2010

Activating WASP mutations associated with X-linked neutropenia result in enhanced actin polymerization, altered cytoskeletal responses, and genomic instability in lymphocytes

Westerberg, L. S., Meelu, P., Baptista, M., Eston, M. A., Adamovich, D. A., Cotta-de-Almeida, V., Seed, B., Rosen, M. K., Vandenberghe, P., Thrasher, A. J., Klein, C., Alt, F. W. & Snapper, S. B., Jun 7 2010, In : Journal of Experimental Medicine. 207, 6, p. 1145-1152 8 p.

Research output: Contribution to journalArticle

37 Scopus citations

A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae

Baxter, R. H. G., Steinert, S., Chelliah, Y., Volohonsky, G., Levashina, E. A. & Deisenhofer, J., Sep 28 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 39, p. 16817-16822 6 p.

Research output: Contribution to journalArticle

38 Scopus citations

A mesoscopic description of contractile cytoskeletal meshworks

Doubrovinski, K., Polyakov, O. & Kaschube, M., Oct 1 2010, In : European Physical Journal E. 33, 2, p. 105-110 6 p.

Research output: Contribution to journalArticle

An interdomain sector mediating allostery in Hsp70 molecular chaperones

Smock, R. G., Rivoire, O., Russ, W. P., Swain, J. F., Leibler, S., Ranganathan, R. & Gierasch, L. M., Oct 6 2010, In : Molecular Systems Biology. 6, 414.

Research output: Contribution to journalArticle

90 Scopus citations

Assessment of linear finite-difference poisson-boltzmann solvers

Wang, J. U. N. & Luo, R. A. Y., Jun 1 2010, In : Journal of Computational Chemistry. 31, 8, p. 1689-1698 10 p.

Research output: Contribution to journalArticle

57 Scopus citations