[NMR paper] Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Related ArticlesIntroducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Comput Struct Biotechnol J. 2020;18:603-611
Authors: Fino R, Byrne R, Softley CA, Sattler M, Schneider G, Popowicz GM
Abstract
NMR-based screening, especially fragment-based drug discovery is a valuable approach in early-stage drug discovery. Monitoring fragment-binding in protein-detected 2D NMR experiments requires analysis of hundreds of spectra to detect chemical shift perturbations (CSPs) in the presence of ligands screened. Computational tools are available that simplify the tracking of CSPs in 2D NMR spectra. However, to the best of our knowledge, an efficient automated tool for the assessment and binning of multiple spectra for ligand binding has not yet been described. We present a novel and fast approach for analysis of multiple 2D HSQC spectra based on machine-learning-driven statistical discrimination. The CSP Analyzer features a C# frontend interfaced to a Python ML classifier. The software allows rapid evaluation of 2D screening data from large number of spectra, reducing user-introduced bias in the evaluation. The CSP Analyzer software package is available on GitHub https://github.com/rubbs14/CSP-Analy...eases/tag/v1.0 under the GPL license 3.0 and is free to use for academic and commercial uses.
NMR-based fragment screening and lead discovery accelerated by principal component analysis
NMR-based fragment screening and lead discovery accelerated by principal component analysis
Abstract
Protein-based NMR spectroscopy has proven to be a very robust method for finding fragment leads to protein targets. However, one limitation of protein-based NMR is that the data acquisition and analysis can be time consuming. In order to streamline the scoring of protein-based NMR fragment screening data and the determination of ligand affinities using 2D NMR experiments we have developed a data analysis workflow based on principal component...
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[NMR paper] Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 (BCL6) BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 (BCL6) BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
Related Articles Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 (BCL6) BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
J Med Chem. 2018 Jul 03;:
Authors: Cheng H, Linhares B, Yu W, Cardenas MG, Ai Y, Jiang W, Winkler A, Cohen S, Melnick A, MacKerell AD, Cierpicki T, Xue F
Abstract
Protein-protein interactions (PPI) between the transcriptional repressor B-cell...
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[NMR paper] Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
J Med Chem. 2016 Apr 14;59(7):3303-10
Authors: Peng C, Frommlet A, Perez M, Cobas C, Blechschmidt A, Dominguez S, Lingel A
Abstract
NMR...
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[NMR paper] NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif Related Articles NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
Acta Pharmacol Sin. 2016 May 30;
Authors: Yu JL, Chen TT, Zhou C, Lian FL, Tang XL, Wen Y, Shen JK, Xu YC, Xiong B, Zhang NX
Abstract
AIM: Fragment-based lead discovery (FBLD) is a complementary approach in drug...
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05-31-2016 09:07 PM
[NMR paper] Automated NMR Fragment Based Screening Identified a Novel Interface Blocker to the LARG/RhoA Complex.
Automated NMR Fragment Based Screening Identified a Novel Interface Blocker to the LARG/RhoA Complex.
Related Articles Automated NMR Fragment Based Screening Identified a Novel Interface Blocker to the LARG/RhoA Complex.
PLoS One. 2014;9(2):e88098
Authors: Gao J, Ma R, Wang W, Wang N, Sasaki R, Snyderman D, Wu J, Ruan K
Abstract
The small GTPase cycles between the inactive GDP form and the activated GTP form, catalyzed by the upstream guanine exchange factors. The modulation of such process by small molecules has been proven to be a...
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Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
J Biomol Screen. 2010 Sep;15(8):978-89
Authors: Kobayashi M, Retra K, Figaroa F, Hollander JG, Ab E, Heetebrij RJ, Irth H, Siegal G
Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing...
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01-13-2011 12:00 PM
[NMR paper] Automated analysis of large sets of heteronuclear correlation spectra in NMR-based dr
Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
Related Articles Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
J Med Chem. 2002 Dec 19;45(26):5649-54
Authors: Damberg CS, Orekhov VY, Billeter M
Drug discovery procedures based on NMR typically require the analysis of thousands of NMR spectra. For example, in "SAR by NMR", two-dimensional NMR spectra are recorded for a target protein mixed with ligand candidates from a comprehensive library of...
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11-24-2010 08:58 PM
[BMNRC community] NMR-based screening: a powerful tool in fragment-based drug discovery
NMR-based screening: a powerful tool in fragment-based drug discovery
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Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
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