Resources

Session 1 - Library Design

Compound libraries:

https://www.tdi.ox.ac.uk/research/research/cellular-high-throughput-screening-hts/libraries-reagents/small-compound-libraries

Fragment Library - Griffiths-Jones 2016 Astex:

https://astx.com/category/discovery/discovery-posters/2016-posters/

Fragment review; Erlanson et al 2016:

https://doi.org/10.1038/nrd.2016.109

Fragment design; Huth et al 2005:

https://doi.org/10.1016/S0076-6879(05)94023-8

PhD Thesis: Dorr, Liam (2013) Interactions of native peptides and small molecules with the PDZ domains of PSD-95 and SAP97.

https://livrepository.liverpool.ac.uk/13955/

PhD Thesis: Pedder, Victoria (2015) Structure-based molecular design: identification of modulators of the NCS1:D2 interaction.

https://livrepository.liverpool.ac.uk/2045039/

Protein Target binding site characterisation (example); Phelan et al 2014:

https://doi.org/10.1042/BST20140082

Fragment Based Drug Discovery; Rees et al 2004

https://doi.org/10.1038/nrd1467

Session 2 - 1D NMR methods

Saturation Transfer Difference (STD)

STD pulse sequence; Mayer & Meyer 2001:

https://doi.org/10.1021/ja0100120

STD review; Meyer & Peters 2003:

https://doi.org/10.1002/anie.200390233

STD Bruker Parameter sets:

Bruker Topspin Pulse Program Catalogue I. 1D & 2D experiments NMR Guide - Topspin 3.0 page 402

WaterLOGSY

WaterLOGSY pulse sequence; Dalvit et al 2000:

https://doi.org/10.1023/A:1008354229396

WaterLOGSY pulse sequence; Dalvit et al 2001:

https://doi.org/10.1023/A:1013302231549

WaterLOGSY example; Raingeval et al 2019:

https://doi.org/10.1080/14756366.2019.1636235

ERETIC2

Bruker Topspin ERECTIC2 manual

19F Examples

19F-ligand 15N-protein; Richards et al 2016:

https://doi.org/10.1038/srep19518

The 3F library: Troelsen et al 2020:

https://doi.org/10.1002/anie.201913125

19F fragment library - Maybridge

https://www.thermofisher.com/uk/en/home/industrial/pharma-biopharma/drug-discovery-development/screening-compounds-libraries-hit-identification/maybridge-fragment-libraries.html

pdf of poster for direct download

Software and standards

CCPN analysis: https://ccpn.ac.uk/

Topspin version 3.5 & 4.0: www.bruker.com

Standard Sample (not necessary for ERETIC):

http://store.bruker.com/products/nmr-reference-standards-for-5mm-probes

Session 3

CCPN Screen V3; tutorials and download:

https://ccpn.ac.uk/software/analysisscreen/

Session 5 - 15N Protein Affinity

Binding Affinity (KD) from chemical shift perturbation review; Williamson 2013:

https://doi.org/10.1016/j.pnmrs.2013.02.001

Binding Affinity (KD) from chemical shift perturbation example; Hobbs et al 2022:

https://doi.org/10.1007/s10858-022-00402-3

Protein:Protein interaction by T2 relaxation; Howard et al 2000:

https://doi.org/10.1006/jmbi.1999.3391

Session 6 - Advanced Methods

Surface Plasmon Resonance (SPR)

SPR explainer; Bakhtiar 2013:

https://dx.doi.org/10.1021/ed200549g

SPR example; Kerr et al 2017:

https://doi.org/10.1074/jbc.M117.795088

Paramagnetic Relaxation Enhancement (PRE)

PRE example; Stott et al 2014:

https://doi.org/10.1074/jbc.M114.591115

Docking

Chemoinformatics review; Kumar et al 2021:

https://doi.org/10.1016/B978-0-12-821748-1.00001-4

Rigid body docking via HADDOCK:

https://wenmr.science.uu.nl/haddock2.4/settings

Competition

1D NMR ligand competition; Dalvit et al 2002:

https://doi.org/10.1021/ja020174b

X-ray Crystallography

NMR & Crystallography example; Wilcken et al 2012 :

https://dx.doi.org/10.1021/ja301056a