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NMR processing:
MDD
NMR assignment:
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Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Old 03-04-2011, 02:19 PM
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Default Lotus Symphony

Lotus Symphony


Even spectroscopists needs an Office suite. Just because I need it infrequently, and there are many free options available, I have chosen one of them. Initially I adopted OpenOffice, then switched to NeoOffice because of its more appealing and sensible graphic interface. The main problem with both of them was that the documents looked different when seen with MS Office. Now I have switched to IBM Lotus Symphony and that problem is solved. Maybe the latest versions of the other programs have improved, but I am so happy with my Symphony that I don't see any reason for trying something different again.
This is a product nobody writes or talk about, so most people confuse it with the original Lotus Symphony suite. The two products have nothing in common but the name. Probably this arguable choice by IBM to recycle the brand was unfortunate: people refuse to even try the new Symphony because they think they already know it.
The new Lotus Symphony is a blend of OpenOffice and Eclipse, topped with a stylish interface. The result is a rare combination of elegance, simplicity and, mainly, intuitiveness: the best virtue of Symphony. Other sure pros are the perfect compatibility with MS Office and the absence of a price.
The main con is the time it takes to start. It really takes an incredible amount of time, about 20 seconds. Afterwards, however, the program seems fast enough for all the things I do. Another limitation is that the suite is not complete. There are four components (word-processor, spreadsheet, presentation program, web browser) and they are very well done, but I need other two programs at least (one for drawing and one for keeping a database). The first three components, however, are really rich in features and this is what really matters. It is far better to have three great programs than to have five not-so-great programs.
There is a problem that I hope will be solved with future releases. If a file contains accented chars in its name (or in the name of any surrounding folder), that file can't be opened. It is necessary to change the name of the file and of its surrounding folders.
Need I tell you that I will never consider the option of using a web-based service instead of a classic desktop application like this? Lotus Symphony does not ignore the web, to tell the truth; it can (optionally) connect to its home servers to let you choose more templates/clip arts or to give you more information. I really like the idea, though I never used those resources, because I find the program extremely intuitive and very easy to use. I have recommended Symphony to my relatives and they all agree with me.


Source: NMR Software blog
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