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Sample preparation:
Proteins
General:
General
Software feature requests
NMR software
Spectrum analysis
Molecular Modeling:
NMR structure calculation
Dynamics by NMR
Structure analysis
Molecular Dynamics
Downloads:
BioNMR downloads
NMR processing:
NMRPipe
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Dynamo
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Amber
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:
TALOS
Preditor
Promega
- Proline
Secondary structure from chemical shifts:
TALOS
MICS
caps, β-turns
d2D
PECAN
CSI
(via RCI server)
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
Agreement with distance restraints:
PROSESS
PSVS
RPF scores
iCing
Agreement with chemical shifts:
PROSESS
CheShift2
Vasco
iCing
Agreement with RDCs:
DC
Anisofit
Agreement with pseudocontact shifts:
Anisofit
Agreement with typical 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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Viewing source for:
NMR Software
[b]NMR Software[/b][list][*][url=http://www.nmrfam.wisc.edu/~volkman/LinuxNMR/programs.html]LinuxNMR[/url] Programs are listed sequentially, according to the normal order of use in a typical NMR structure determination project. Rather than providing detailed tutorials on the use of the various programs, a few comments on the general use of each program are provided, as well as the literature citations and links to the original documentation. [b]Auto-assignment programs [/b] [*][url=http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html#AutoAssign]AutoAssign[/url] AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins. Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M., Shimotakahara, S., Chien, C., Powers, R., Montelione, G.T., J. Mol. Biol. 269, 592-610 (1997). [b]Data processing[/b] [*][url=http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html#AutoProc]AutoProc[/url] AutoProc is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. The programs are written in Perl and make use of ASCII tables that the user can modify. In the current implementation, NMRPipe (Delaglio, et al. J. Biomol. NMR, 1995, 277-293) are automatically generated based on Pulse Sequence-dependent and Spectrometer-dependent information found in the tables. A Varian to NMRPipe conversion script generator (with automatic referencing) is also part of the AutoProc package. M. Bayro, D. Monleon, M.C. Baran, G. Sahota, R. Paranji, H.N.B. Moseley, J.M. Aramini, G.V.T. Swapna, G.T. Montelione, "Simple and Rapid Processing of Multidimensional NMR Spectra Using AutoProc and NMRPipe Software", (in preparation). [*][url=http://www.bio.cam.ac.uk/azara/]AZARA[/url] NMR processing, manipulation and viewing software written by Wayne Boucher. [*][url=http://www.nmr.kun.nl/bfc/Software/procTool/procTool.html]procTool: nmrPipe interface tool[/url] ProcTool is an nmrPipe interface tool, designed for easy spectral processing of NMR data. Using predefined and logically ordered fields, parameters can be entered, modified and nmrPipe conversion and processing scripts can be generated and executed. Settings, processing scripts, and a history are stored in a single file, ready for easy reproduction at any stage. [b]Spectra display and analysis [/b] [*][url=http://www-ccmr-nmr.bioc.cam.ac.uk/public/ANSIG/ansig.html]ANSIG[/url] ANSIG version 3.3 Assignment of NMR Spectra by Interactive Graphics. A program written in Fortran 77 for Silicon Graphics machines. Copyright 1996 Per Kraulis [b]NMR data management [/b] [*][url=http://www.nmr.kun.nl/bfc/Software/procTool/nmrManage.html]nmrManage: project management tool[/url] The nmrManage program is designed to group sets of related procTool files and sample files in one place in so-called projects, without actually moving or copying data. Thus, it is an indirection mechanism (pointer mechamism). Using nmrManage, one can quickly view, modify, or list the different experiments or samples. [/list]
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