KPWU blog Things must be changed before Protein-RNA docking using Haddock

		BioNMR > NMR community > News from NMR blogs
[KPWU blog] Things must be changed before Protein-RNA docking using Haddock

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-23-2012, 07:38 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,185

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

Things must be changed before Protein-RNA docking using Haddock

Things must be changed before Protein-RNA docking using Haddock

Just a note for RNA-protein docking using Haddock 2.1 System: Mac OS 10.6.8, CNS 1.3, Haddock 2.1 1. RNA (or DNA) nomenclature in CNS is not same as the names in PDB. e.g. ACU in PDB = ADE CYT URI in CNS The “nucleic acid builder” developed in David *Case group can generate template structure [...]

Go to KPWU blog to read complete post.

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Three-days HADDOCK workshop in Vilnius LINK Description HADDOCK is an information-driven docking program developed at Utrecht University, which is widely used in the structural biology community and has demonstrated a strong performance in the blind docking competition CAPRI. The workshop will be given by Prof. Alexandre Bonvin with a number of his group members. It will consist of lectures in the morning and hands-on sessions on computers in the afternoon. Sign ups are limited to 20 people. For these, experience with Linux is a requisite. The workshop will cover various aspects of the modelling of biomolecular...	markber	Conferences	0	02-26-2012 10:22 PM
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking - 7thSpace Interactive (press release) DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking 7thSpace Interactive (press release) Unfortunately, the experimental determination of protein-RNA complexes is tedious and difficult, both by X-ray crystallography and NMR. For many interacting proteins and RNAs the individual structures are available, enabling computational prediction of ... Read here	nmrlearner	Online News	0	08-19-2011 04:02 AM
[KPWU blog] HADDOCK on iMac and a quick benchmark HADDOCK on iMac and a quick benchmark Recently I requested a copy of HADDOCK from Dr. Alexandre Bonvin in order to generate some docked dimers for my colleagues. They are working on some dimeric proteins but they have no idea how to obtain the dimeric conformation from homologous known structures. I spent few days reading the threads in the HADDOCK discussion group http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=285&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	03-29-2011 09:01 PM
[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins. 2005 Aug 15;60(3):367-81 Authors: van Dijk AD, Fushman D, Bonvin AM When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Docking multiple conformations of a flexible ligand into a protein binding site using Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Related Articles Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Proteins. 2002 Feb 15;46(3):295-307 Authors: Zabell AP, Post CB A method is described for docking a large, flexible ligand using intra-ligand conformational restraints from exchange-transferred NOE (etNOE) data. Numerous conformations of the ligand are generated in isolation, and a subset of representative conformations is...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Structure prediction of protein complexes by an NMR-based protein docking algorithm. Structure prediction of protein complexes by an NMR-based protein docking algorithm. Related Articles Structure prediction of protein complexes by an NMR-based protein docking algorithm. J Biomol NMR. 2001 May;20(1):15-21 Authors: Kohlbache O, Burchardt A, Moll A, Hildebrandt A, Bayer P, Lenhof HP Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[BMNRC community] HADDOCK Software web portal HADDOCK Software web portal http://haddock.chem.uu.nl/index.html Go to BMNRC community to find more info about this topic.	nmrlearner	News from other NMR forums	0	09-02-2010 04:59 AM

« 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 Off Trackbacks are Off Pingbacks are Off Refbacks are Off