 Connection
John Markley to Software
This is a "connection" page, showing publications John Markley has written about Software.
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Connection Strength |
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4.904 |
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Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL. Increasing rigor in NMR-based metabolomics through validated and open source tools. Curr Opin Biotechnol. 2017 02; 43:56-61.
Score: 0.333
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Stark JL, Eghbalnia HR, Lee W, Westler WM, Markley JL. NMRmix: A Tool for the Optimization of Compound Mixtures in 1D (1)H NMR Ligand Affinity Screens. J Proteome Res. 2016 Apr 01; 15(4):1360-8.
Score: 0.322
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Chen VB, Wedell JR, Wenger RK, Ulrich EL, Markley JL. MolProbity for the masses-of data. J Biomol NMR. 2015 Sep; 63(1):77-83.
Score: 0.307
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Dashti H, Tonelli M, Markley JL. ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment. J Biomol NMR. 2015 Jul; 62(3):247-52.
Score: 0.304
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Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. J Biomol NMR. 2015 Aug; 62(4):481-95.
Score: 0.302
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Lee W, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015 Apr 15; 31(8):1325-7.
Score: 0.294
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Lee W, Stark JL, Markley JL. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR. 2014 Nov; 60(2-3):73-5.
Score: 0.289
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Lee W, Bahrami A, Markley JL. ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. Bioinformatics. 2013 Feb 15; 29(4):515-7.
Score: 0.256
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Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR. 2012 Oct; 54(2):169-79.
Score: 0.251
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Bahrami A, Tonelli M, Sahu SC, Singarapu KK, Eghbalnia HR, Markley JL. Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR. PLoS One. 2012; 7(3):e33173.
Score: 0.243
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Lee W, Kim JH, Westler WM, Markley JL. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics. 2011 Jun 15; 27(12):1727-8.
Score: 0.229
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Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009 Aug 15; 25(16):2085-7.
Score: 0.201
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Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Veglia G, Markley JL, Melacini G, Lee W. CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinformatics. 2021 05 23; 37(8):1176-1177.
Score: 0.115
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Rahimi M, Lee Y, Markley JL, Lee W. iPick: Multiprocessing software for integrated NMR signal detection and validation. J Magn Reson. 2021 07; 328:106995.
Score: 0.115
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Weber DK, Wang S, Markley JL, Veglia G, Lee W. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020 05 01; 36(9):2915-2916.
Score: 0.107
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Romero PR, Kobayashi N, Wedell JR, Baskaran K, Iwata T, Yokochi M, Maziuk D, Yao H, Fujiwara T, Kurusu G, Ulrich EL, Hoch JC, Markley JL. BioMagResBank (BMRB) as a Resource for Structural Biology. Methods Mol Biol. 2020; 2112:187-218.
Score: 0.104
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Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol. 2019 Apr 01; 75(Pt 4):451-454.
Score: 0.099
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Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. J Biomol NMR. 2019 Feb; 73(1-2):5-9.
Score: 0.097
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Lee W, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2018 05 01; 34(9):1586-1588.
Score: 0.093
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Markley JL. Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules. Adv Exp Med Biol. 2018; 1105:43-58.
Score: 0.091
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Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR. 2016 06; 65(2):51-7.
Score: 0.081
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Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. Integrative NMR for biomolecular research. J Biomol NMR. 2016 04; 64(4):307-32.
Score: 0.081
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Olson JB, Markley JL. Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package. J Biomol NMR. 1994 May; 4(3):385-410.
Score: 0.071
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Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers. J Magn Reson. 2013 Nov; 236:83-8.
Score: 0.067
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Kobayashi N, Harano Y, Tochio N, Nakatani E, Kigawa T, Yokoyama S, Mading S, Ulrich EL, Markley JL, Akutsu H, Fujiwara T. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database. J Biomol NMR. 2012 Aug; 53(4):311-20.
Score: 0.062
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Chylla RA, Hu K, Ellinger JJ, Markley JL. Deconvolution of two-dimensional NMR spectra by fast maximum likelihood reconstruction: application to quantitative metabolomics. Anal Chem. 2011 Jun 15; 83(12):4871-80.
Score: 0.058
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Lewis IA, Schommer SC, Markley JL. rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magn Reson Chem. 2009 Dec; 47 Suppl 1:S123-6.
Score: 0.052
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Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol. 2008 Feb; 26(2):162-4.
Score: 0.046
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Markley JL, Anderson ME, Cui Q, Eghbalnia HR, Lewis IA, Hegeman AD, Li J, Schulte CF, Sussman MR, Westler WM, Ulrich EL, Zolnai Z. New bioinformatics resources for metabolomics. Pac Symp Biocomput. 2007; 157-68.
Score: 0.042
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Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AM, Kaptein R, Markley JL, Ulrich EL. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J Biomol NMR. 2005 May; 32(1):1-12.
Score: 0.038
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Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR. 2005 May; 32(1):71-81.
Score: 0.038
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Dashti H, Westler WM, Wedell JR, Demler OV, Eghbalnia HR, Markley JL, Mora S. Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. Sci Data. 2020 07 03; 7(1):210.
Score: 0.027
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Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR. Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening. Anal Chem. 2017 11 21; 89(22):12201-12208.
Score: 0.023
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Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol. 2015 Jun; 22(6):433-4.
Score: 0.019
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Takeda M, Hallenga K, Shigezane M, Waelchli M, Löhr F, Markley JL, Kainosho M. Construction and performance of an NMR tube with a sample cavity formed within magnetic susceptibility-matched glass. J Magn Reson. 2011 Apr; 209(2):167-73.
Score: 0.014
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Pan X, Wesenberg GE, Markley JL, Fox BG, Phillips GN, Bingman CA. A graphical approach to tracking and reporting target status in structural genomics. J Struct Funct Genomics. 2007 Dec; 8(4):209-16.
Score: 0.011
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Cornilescu G, Bahrami A, Tonelli M, Markley JL, Eghbalnia HR. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections. J Biomol NMR. 2007 Aug; 38(4):341-51.
Score: 0.011
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Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR. 2003 Jun; 26(2):139-46.
Score: 0.008
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Stockman BJ, Krezel AM, Markley JL, Leonhardt KG, Straus NA. Hydrogen-1, carbon-13, and nitrogen-15 NMR spectroscopy of Anabaena 7120 flavodoxin: assignment of beta-sheet and flavin binding site resonances and analysis of protein-flavin interactions. Biochemistry. 1990 Oct 16; 29(41):9600-9.
Score: 0.003
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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