[ASAP] Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw

		BioNMR > Educational resources > Journal club
[ASAP] Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw

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

07-16-2022, 01:22 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

[ASAP] Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw

[ASAP] Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw

Biochemistry
DOI: 10.1021/acs.biochem.2c00188

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[ASAP] Efficient Exploration of Sequence Space by Sequence-Guided Protein Engineering and Design Efficient Exploration of Sequence Space by Sequence-Guided Protein Engineering and Design https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00757/20220304/images/medium/bi1c00757_0005.gif Biochemistry DOI: 10.1021/acs.biochem.1c00757 More...	nmrlearner	Journal club	0	03-05-2022 01:44 AM
[ASAP] Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs) Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs) https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00714/20220110/images/medium/bi1c00714_0006.gif Biochemistry DOI: 10.1021/acs.biochem.1c00714 More...	nmrlearner	Journal club	0	01-11-2022 06:11 PM
[ASAP] Protein Engineering in the Design of Protein–Protein Interactions: SARS-CoV-2 Inhibitors as a Test Case Protein Engineering in the Design of Protein–Protein Interactions: SARS-CoV-2 Inhibitors as a Test Case https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00356/20210701/images/medium/bi1c00356_0003.gif Biochemistry DOI: 10.1021/acs.biochem.1c00356 http://feeds.feedburner.com/~r/acs/bichaw/~4/I1umUsCPml8 More...	nmrlearner	Journal club	0	07-03-2021 08:12 PM
[ASAP] Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.0c00484/20200924/images/medium/bi0c00484_0007.gif Biochemistry DOI: 10.1021/acs.biochem.0c00484 http://feeds.feedburner.com/~r/acs/bichaw/~4/ZWnwIs0C-lk More...	nmrlearner	Journal club	0	09-26-2020 07:23 AM
[ASAP] Engineering Order and Cooperativity in a Disordered Protein Engineering Order and Cooperativity in a Disordered Protein https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.9b00182/20190430/images/medium/bi-2019-00182k_0001.gif Biochemistry DOI: 10.1021/acs.biochem.9b00182 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/KFOtQC1Ujw8 More...	nmrlearner	Journal club	0	05-01-2019 08:17 AM
Final piece of protein puzzle: NMR tops and tails HIV Final piece of protein puzzle: NMR tops and tails HIV http://www.spectroscopynow.com/common/images/thumbnails/15f6ce91e6f.jpgNuclear magnetic resonance (NMR) spectroscopy has been used to put in place the final piece of the HIV-1 protein structure, the cytoplasmic tail of gp41 protein. The research by a team at the University of Alabama at Birmingham led by Jamil Saad will help scientists better understand how the virus infects human cells and how progeny viruses are assembled and released from infected cells. Read the rest at Spectroscopynow.com	nmrlearner	General	0	11-01-2017 05:51 AM
[NMR paper] NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins. NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary_FullTextOnline_120x27.gif Related Articles NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins. FEBS J. 2015 Jan;282(2):341-60 Authors: Carbajo RJ, Sanz L, Perez A, Calvete JJ Abstract Extant disintegrins, as found in the venoms of Viperidae and...	nmrlearner	Journal club	0	04-01-2015 09:00 PM
[Question from NMRWiki Q&A forum] peak missing in nh hsqc protein nmr peak missing in nh hsqc protein nmr Dear NMR wikiers iam assigning 95 aminoacid residue protein . i can see 76 cross peaks in hsqc on 700 vnmr cryob . still some peaks are missing . i tried at modified ph conditions , buffer ionic strength and d2o percentage ( 5 to 10 percent ).but no significant improvement is their any experment to get best number of cross peaks in hsqc ?	nmrlearner	News from other NMR forums	0	06-28-2011 04:40 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