sci-chemistry / parassign

Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)

Official package sites : http://protchem.lic.leidenuniv.nl/software/parassign/registration ·

The use of paramagnetic NMR data for the refinement of structures of proteins and protein complexes is widespread. However, the power of paramagnetism for protein assignment has not yet been fully exploited. PARAssign is software that uses pseudocontact shift data derived from several paramagnetic centers attached to the protein to obtain amide and methyl assignments. The ability of PARAssign to perform assignment when the positions of the paramagnetic centers are known and unknown is demonstrated. PARAssign has been tested using synthetic data for methyl assignment of a 47 kDa protein, and using both synthetic and experimental data for amide assignment of a 14 kDa protein. The complex fitting space involved in such an assignment procedure necessitates that good starting conditions are found, both regarding placement and strength of paramagnetic centers. These starting conditions are obtained through automated tensor placement and user-defined tensor parameters. The results presented herein demonstrate that PARAssign is able to successfully perform resonance assignment in large systems with a high degree of reliability. This software provides a method for obtaining the assignments of large systems, which may previously have been unassignable, by using 2D NMR spectral data and a known protein structure.

v20130522 :: 0 :: gentoo (Masked by set 3553)

Modified
License
Apache-2.0
Keywords
~amd64 ~amd64-linux ~x86 ~x86-linux

python_targets

python2_7
Build with Python 2.7

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

dev-python / cython : A Python to C compiler

dev-python / matplotlib : Pure python plotting library with matlab like syntax

dev-python / numpy : Fast array and numerical python library

dev-python / scientificpython : Scientific Module for Python

sci-biology / biopython : Python modules for computational molecular biology

sci-libs / scipy : Scientific algorithms library for Python

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper


3553
Michał Górny
Ancient vulnerable version of NumPy, plus all its revdeps. Removal in 30 days. Bug #627962.
  • <dev-python/numpy-1.14.5
  • dev-python/pyclimate
  • dev-python/scientificpython
  • sci-chemistry/parassign
  • sci-chemistry/pymol-plugins-psico
  • sci-libs/mmtk
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Justin Lecher · gentoo
Drop deprecated usage of parallel python eclass functions
Python eclasses dropped parallel execution support some while ago. python_parallel_foreach_impl was an alias for python_foreach_impl for some time already. Signed-off-by: Justin Lecher <jlec@gentoo.org>
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed