NMR paper A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands

		BioNMR > Educational resources > Journal club
[NMR paper] A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

09-07-2022, 04:33 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands

A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands

Cadherins promote cell-cell adhesion by forming homophilic interactions via their N-terminal extracellular domains. Hence, they have broad-ranging physiological effects on tissue organization and homeostasis. When dysregulated, cadherins contribute to different aspects of cancer progression and metastasis; therefore, targeting the cadherin adhesive interface with small-molecule antagonists is expected to have potential therapeutic and diagnostic value. Here, we used molecular docking simulations...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment - Wiley NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment - Wiley NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment Wiley Read here	nmrlearner	Online News	0	11-02-2021 07:28 AM
NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment - Wiley NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment - Wiley NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment Wiley Read here	nmrlearner	Online News	0	10-01-2021 02:15 AM
NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment - Wiley NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment - Wiley NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment Wiley Read here	nmrlearner	Online News	0	09-29-2021 12:23 PM
[NMR paper] NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment The main protease (3CLp) of the SARS-CoV-2, the causative agent for the COVID-19 pandemic, is one of the main targets for drug development. To be active, 3CLp relies on a complex interplay between dimerization, active site flexibility, and allosteric regulation. The deciphering of these mechanisms is a crucial step to enable the search for inhibitors. In this context, using NMR spectroscopy, we studied the conformation of dimeric 3CLp from the...	nmrlearner	Journal club	0	09-29-2021 12:23 PM
[NMR paper] A Photoaffinity-Based Fragment-Screening Platform for Efficient Identification of Protein Ligands A Photoaffinity-Based Fragment-Screening Platform for Efficient Identification of Protein Ligands Angewandte Chemie International Edition, Volume 59, Issue 47, Page 21096-21105, November 16, 2020. More...	nmrlearner	Journal club	0	11-10-2020 10:50 AM
[NMR paper] A Ligand-Based NMR Screening Approach for the Identification and Characterization of Inhibitors and Promoters of Amyloid Peptide Aggregation. A Ligand-Based NMR Screening Approach for the Identification and Characterization of Inhibitors and Promoters of Amyloid Peptide Aggregation. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles A Ligand-Based NMR Screening Approach for the Identification and Characterization of Inhibitors and Promoters of Amyloid Peptide Aggregation. ChemMedChem. 2017 Sep 07;12(17):1458-1463 Authors: Dalvit C, Santi S, Neier R Abstract Over the...	nmrlearner	Journal club	0	09-24-2017 06:16 AM
Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00153/20170721/images/medium/bi-2017-00153s_0009.gif Biochemistry DOI: 10.1021/acs.biochem.7b00153 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/mhk6q86DgOU More...	nmrlearner	Journal club	0	07-22-2017 05:57 AM
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...	nmrlearner	Journal club	0	01-13-2011 12:00 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off