Protein Structure Prediction: Threading & Homology Modeling - Thomas Steinke

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CS23D - generating protein structure from NMR chemical shifts and sequence homology CS23D website CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. CS23D uses a combination of maximal subfragment assembly, chemical shift threading, shift-based torsion angle prediction and chemical shift refinement to generate and refine the protein coordinates. CS23D accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein normally within 10-15 minutes (3 hours max). CS23D performance is dependent on the completeness of the chemical shift assignments and...	markber	NMR software	0	02-23-2012 08:40 PM
nmrwiki: RT @kiharalab: Postdoc position available in area of protein structure modeling/prediction at Kihara Lab, Purdue Univ http://bit.ly/hfuM ... nmrwiki: RT @kiharalab: Postdoc position available in area of protein structure modeling/prediction at Kihara Lab, Purdue Univ http://bit.ly/hfuM ... nmrwiki: RT @kiharalab: Postdoc position available in area of protein structure modeling/prediction at Kihara Lab, Purdue Univ http://bit.ly/hfuM ... Source: NMRWiki tweets	nmrlearner	Job marketplace	0	04-25-2011 03:43 AM
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†). Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†). Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†). J Med Chem. 2011 Jan 27; Authors: Orcajo-Rinco?n AL, Ortega-Gutie?rrez S, Serrano P, Torrecillas IR, Wu?thrich K, Campillo M, Pardo L, Viso A, Benhamu? B, Lo?pez-Rodri?guez ML We report a novel series of non-peptide ligands that inhibit the growth...	nmrlearner	Journal club	0	01-29-2011 11:35 AM
[NMR paper] NMR solution structure, backbone mobility, and homology modeling of c-type cytochrome NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria. Related Articles NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria. Chembiochem. 2002 Apr 2;3(4):299-310 Authors: Banci L, Bertini I, Ciurli S, Dikiy A, Dittmer J, Rosato A, Sciara G, Thompsett AR The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the...	nmrlearner	Journal club	0	11-24-2010 07:49 PM
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[NMR paper] A computational method for NMR-constrained protein threading. A computational method for NMR-constrained protein threading. Related Articles A computational method for NMR-constrained protein threading. J Comput Biol. 2000;7(3-4):449-67 Authors: Xu Y, Xu D, Crawford OH, Einstein JR Protein threading provides an effective method for fold recognition and backbone structure prediction. But its application is currently limited due to its level of prediction accuracy and scope of applicability. One way to significantly improve its usefulness is through the incorporation of underconstrained (or partial) NMR...	nmrlearner	Journal club	0	11-18-2010 08:15 PM
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[NMR paper] A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of s A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry. 1996 Apr 9;35(14):4540-50 Authors: Modi S, Paine MJ, Sutcliffe MJ, Lian LY, Primrose WU, Wolf CR, Roberts GC The cytochrome P450 responsible for the debrisoquine/sparteine polymorphism (P450 2D6) has been produced in large...	nmrlearner	Journal club	0	08-22-2010 02:27 PM

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