Nature News

De novo protein design by scientific residents


Lintott, C.J. et al. Galaxy Zoo: morphologies derived from the visible inspection of galaxies from the Sloan Digital Sky Survey. Mon. Don’t. R. Astron. Soc. 389, 1179-1189 (2008).


Kim, J. S. et al. The specificity of space-time wiring helps selectivity of route within the retina. Nature 509, 331-336 (2014).


Kawrykow, A. et al. Phylo: a citizen method to enhance the alignment of a number of sequences. PLoS ONE 7, e31362 (2012).


Lee, J. et al. The RNA design guidelines come from a large open laboratory Proc. Natl Acad. Sci. USA 111, 2122-2127 (2014).


Cooper, S. et al. Predict protein buildings with a web-based multiplayer sport. Nature 466, 756-760 (2010).


Epstein, C.J., Goldberger, R.F. & Anfinsen, C.B. Genetic management of the tertiary protein construction: research on mannequin programs. Chilly Harb Spring. Symp. As. Biol. 28, 439-449 (1963).


Lin, Y.-R. et al. Management of the overall form and dimension of de novo designed proteins. Proc. Natl Acad. Sci. USA 112, E5478 to E5485 (2015).


Huang, P.-S., Boyken, S.E. and Baker, D. The arrival on the age of de novo protein design. Nature 537, 320-327 (2016).


Marcos, E. et al. Rules of protein design with cavities fashioned of curved β sheets. Science 355, 201-206 (2017).


Dou, J. et al. De novo design of a β-canon activating fluorescence. Nature 561, 485-491 (2018).


Alford, R.F. et al. The vitality perform any Rosetta atom for macromolecular modeling and design. J. Chem. Comput Concept. 13, 3031-3048 (2017).


Khatib, F. et al. Crystal construction of a monomeric retroviral protease resolved by gamers who play protein folding. Nat. Struct. Mol. Biol. 18, 1175-1177 (2011).


Eiben, C.B. et al. Elevated exercise Diels – Alderase by a backbone transforming guided by Foldit gamers. Nat. Biotechnol. 30, 190-192 (2012).


Blout, E.R. & Idelson, M. Results of the composition on the configuration of water-soluble polypeptide copolymers of 1-glutamic acid and l-lysine. Jam. Chem. Soc. 80, 4909-4913 (1958).


Doty, P., Imahori, Okay. & Klemperer, E. Resolution properties and configurations of a polyampholytic polypeptide: copoly-l-lysine-1-glutamic acid. Proc. Natl Acad. Sci. USA 44, 424-431 (1958).


Ghosh, Okay. & Dill, Okay. A. Concept of cooperative protein folding: helical bundles. Jam. Chem. Soc. 131, 2306-22312 (2009).


Rohl, C.A., Strauss, C.Em., Misura, Okay.M.S. & Baker, D. Prediction of Protein Construction Utilizing Rosetta. Enzymol strategies. 383, 66-93 (2004).


Koga, N. et al. Rules of designing perfect protein buildings. Nature 491, 222-227 (2012).


Regan, L. & DeGrado, W. F. Characterization of a helical protein designed from the primary ideas. Science 241, 976-978 (1988).


Harbury, P.B., Plecs, J.J., B. Tidor, Alber, T. and Kim, P. S. Excessive-resolution protein design with skeletal freedom. Science 282, 1462-1467 (1998).


Thomson, A. R. et al. Laptop design of water-soluble helical barrels. Science 346, 485-488 (2014).


Jacobs, T. M. et al. Structurally distinct protein design utilizing methods impressed by evolution. Science 352, 687-690 (2016).


Ramachandran, G.N. & Sasisekharan, V. Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283-438 (1968).


Chen, V.B. et al. MolProbity: validation of the construction any atom for macromolecular crystallography. Acta Crystallogr. D 66, 12-21 (2010).


Montelione, G. T. et al. Suggestions of the WwPDB NMR Validation Working Group. Construction 21, 1563-1570 (2013).


Zhang, Y. & Skolnick, J.TM-align: an algorithm for aligning the construction of a protein primarily based on TM rating. Nucleic Acids Res. 33, 2302-2309 (2005).


Santoro, M. M. & Bolen, D. W. Unfolding free vitality modifications decided by the linear extrapolation technique. 1. Sequence of phenylmethanesulfonyl α-chymotrypsin utilizing completely different denaturants. Biochemistry 27, 8063-8068 (1988).


Otwinowski, Z. & Minor, W. Remedy of X-ray diffraction knowledge collected in oscillation mode. Enzymol strategies. 276, 307-326 (1997).


McCoy, A.J. et al. Phaser crystallographic software program. J. Appl. Cristallogr. 40, 658-674 (2007).


Emsley, P., Lohkamp, ​​B., Scott, W. G. and Cowtan, Okay. Traits and improvement of Coot. Acta Crystallogr. D 66, 486-501 (2010).


Afonine, P.V. et al. In the direction of an automatic refinement of the crystallographic construction with phenix.refine. Acta Crystallogr. D 68, 352-367 (2012).


Jansson, M. et al. Excessive stage manufacturing of uniformly enriched fusion proteins in 15N and 13C in Escherichia coli. J. Biomol. NMR 7, 131-141 (1996).


Delaglio, F. et al. NMRPipe: multidimensional spectral processing system primarily based on UNIX tubes. J. Biomol. NMR 6, 277-293 (1995).


Bartels, C., Xia, T.H., Billeter, M., Güntert, P. & Wüthrich, Okay. The XEASY program for computer-aided NMR spectral evaluation of organic macromolecules. J. Biomol. RMN 6.1-10 (1995).


Liu, G. et al. Protocol for the gathering and evaluation of NMR knowledge for the dedication of the excessive throughput protein construction. Proc. Natl Acad. Sci. USA 102, 10487-10492 (2005).


Shen, Y., Delaglio, F., Cornilescu, G. & Bax, A. TALOS +: a hybrid technique for predicting the torsion angles of the protein skeleton from chemical shifts in NMR. J. Biomol. NMR 44, 213-223 (2009).


Huang, Y.J., Tejero, R., Powers, R. and Montelione, G. T. A topology constrained distance community algorithm for the dedication of protein construction from NOESY knowledge. Proteins 62, 587-603 (2006).


Güntert, P., Mumenthaler, C. and Wüthrich, Okay. Dynamics of the torsion angle for the calculation of the NMR construction with the brand new DYANA program. J. Mol. Biol. 273, 283-298 (1997).


Herrmann, T., Güntert, P. & Wüthrich, Okay. Dedication of protein NMR construction with computerized allocation of NOE utilizing new CANDID software program and dynamics algorithm. torsion angle DYANA. J. Mol. Biol. 319, 209-227 (2002).


Huang, YJ, Powers, R. and Montelione, GT Scores of Reminder, Precision and F-measure in NMR (FPR scores): construction of high quality evaluation measures primarily based on statistics of extraction d & # 39; info. Jam. Chem. Soc. 127, 1665-1674 (2005).


Linen, J.P., Williams, M.A., Spronk, C.A., Bonvin, A.M. & Nilges, M. Refinement of protein buildings in an express solvent. Proteins 50, 496-506 (2003).


Brünger, A. T. et al. Crystallography and NMR system: a brand new software program suite for the dedication of the macromolecular construction. Acta Crystallogr. D 54, 905-921 (1998).


Luthy, R., Bowie, J. U. and Eisenberg, D. Analysis of protein fashions with three-dimensional profiles. Nature 356, 83-85 (1992).


Sippl, M. J. Recognition of errors within the three-dimensional buildings of proteins. Proteins 17, 355-362 (1993).


Laskowski, R. A., Macarthur, M.W., Moss, D.S. and Thornton, J.M. Procheck – a program to confirm stereochemical high quality of protein buildings. J. Appl. Cristallogr. 26, 283-291 (1993).


Phrase, J.M., Bateman, R.C., Jr., Presley, B.Okay., Lovell, S.C. and Richardson, D.C. Protein Sci. 9, 2251-2259 (2000).


Bhattacharya, A., Tejero, R. and Montelione, G. T. Analysis of protein buildings decided by structural genomic consortia. Proteins 66, 778-795 (2007).


Tejero, R., D. Snyder, B. Mao, Aramini, J.M. and Montelione, G. T. PDBStat: common stress conversion software program and stress evaluation software program for protein NMR. J. Biomol. NMR 56, 337-351 (2013).


Trifonov, E. N. in Construction and Strategies, Vol. 1: The Acts of the sixth dialog held on the College – SUNY (Adenine, 1990).


Holm, L. and Laakso, L. M. Dali server replace. Nucleic Acids Res. 44 (W1), W351 to W355 (2016).

Leave a Reply

Your email address will not be published. Required fields are marked *