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 [...]
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)
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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.
Things must be changed before Protein-RNA docking using Haddock
Linear Mode
