CABM NMR Software

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CABM AutoNMR Software
NMR Lab Software

AutoAssign logo

Autoassign (c) 1998, 1999, 2002 D.E. Zimmerman, H.N.B. Moseley, C.A. Kulikowski, G.T. Montelione and Rutgers, The State University of New Jersey. 

AutoPeak (c) 2001, 2002, 2003 H. N. B. Moseley, G. T. Montelione and Rutgers, The State University of New Jersey.

Assignment Validation Software (c) 2003 H. N. B. Moseley, G. T. Montelione and Rutgers, The State University of New Jersey.

AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins. Originally developed in the Lisp programming language [1] the current version of AutoAssign includes a C++ server supported for SGI computer systems, together with a graphical user interface implemented in Java for multiplatform use.   The C++/Java AutoAssign automates the assignments of HN, NH, CO, C-alpha, C-beta, and H-alpha resonances from a set of peak-picked triple-resonance NMR spectra[1].  Test data provided with the program include several independently-collected triple-resonance NMR peak lists for proteins ranging in size from ~6 to ~18 kD.  With these real data, AutoAssign obtains nearly complete resonance assignments (~98%) with virtually no errors (< 0.5%).  The constraint-based algorithm limits assignments to only those with significant evidence. AutoAssign performs the automated analysis of backbone resonance assignments in only seconds on current RISC and Pentium-based platforms.

[1] 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). 

AutoAssign is available for SGI IRIX and Redhat Linux platforms.
You can download a license agreement (in pdf format).
AutoAssign Citations


AutoStructure/AutoQF

AutoStructure logo
We formulated the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and developed a novel topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite which implements this topology-constrained distance network analysis algorithm and iteratively generates structures using the three-dimension (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks.

Program AutoQF assesses the quality of input data and final 3D structures using a statistical measure of goodness-of-fit with the input data, F-measure. The input for AutoStructure includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D, and/or 4D-NOESY cross peaks, and the query structure(s).

[1] Huang Y.J., Swapana, G.V., Rajan, P.K., Ke, H, Xia, B., Shukla, K., Inouye, M. & Montelione, G.T. (2003). Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli. J Mol Biol 327, 521-36

AutoStructure/AutoQF is only available for Redhat Linux platform.
You can download a license agreement (in pdf format). The distribution includes Hyper, PDBStat, and AutoQF as part of the AutoStructure software package.

Go to AutoStructure Homepage

AutoProc

AutoProc logo
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).

You can download a license agreement (in pdf form).


HOMA: HOmology Modeling Automatically

Homology model of RBP-MS
HOMA
We have described an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures  Li et al, Protein Science, 6, 956-970, 1997

This method uses distances calculated from the template structure to determine the structure of a homologous protein. This software calculates distances between atoms in the template structure from a pdb file and then, uses a sequence alignment file to select the distance constraints involving homologous atoms. 

HOMA is a user-friendly, web-based implementation of this algorithm. HOMA requires an alignment of the template sequence against the query sequence and a template coordinate file to carry out the calculations. The results include a bundle of models as well as analysis of the model quality.

HOMA is available at http://www-nmr.cabm.rutgers.edu/HOMA/ or http://hyper.quifis.uv.es/HOMA/index.html, under password protection.

Hyper

Nine distances used by HYPER
HYPER
A hierarchical algorithm involving progressive application of conformational constraints for automatic determination of protein dihedral angles and C(beta)H2 methylene resonance assignments from NMR data.

(c) Copyright 1994-1997 Roberto Tejero and Gaetano T. Montelione 
Center for Advanced Technology and Medicine (CABM) 
Rutgers University

Hyper computes the set of phi, psi and chi1 dihedral angles and C(beta)H2 stereospecific assignments that are consitent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative sclar coupling constant bounds.

Please read the README for further description.

You can download a license agreement (in pdf format). The distribution includes Hyper, PDBStat, and AutoQF as part of the AutoStructure software package.


PDBStat

Superposition of ZDomain made by PDBSTAT
PDBSTAT
PDBStat evaluates some statistics of biomacromolecules given the cartesian coordinates.

(c) Copyright 1992-1997 Roberto Tejero and Gaetano T. Montelione 
Center for Advanced Technology and Medicine (CABM) 
Rutgers University

Pdbstat is a program to evaluate some statistics of biomacromolecules given the cartesian coordinates. It can be also used to prepare some input files needed for othe software packages like CONGEN in structure determination from NMR data. It can read a family of structures and evaluate rmsd's and optimal superposition.

Please read the README for further description.

You can download a license agreement (in pdf format). The distribution includes Hyper, PDBStat, and AutoQF as part of the AutoStructure software package.


SPINS logo
(c) Copyright 2002  Michael C. Baran and Gaetano T. Montelione
Center for Advanced Technology and Medicine (CABM)
Rutgers University

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB).  The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system.

Baran, M.; Moseley, H.N.B.; Sahota, G.; Montelione, G.T.  J. Biomol. NMR 2002, 24: 113-121.  SPINS: Standardized ProteIn NMR Storage.  A data dictionary and object-oriented relational database for archiving protein NMR spectra.

The SPINS project is evolving into an integrated software solution to the NMR structural determination process.  SPINS interacts with over 20 different pieces of NMR software providing users with a highly integrated approach to automated data collection management, NMR data processing, peak-picking, spin-typing, resonance assignments, side-chain assignments, structural determination, as well numerous validation and reporting tools.
You can download a license agreement (in pdf format).


ZebaView

With the completion of several genome sequencing projects, much of the emphasis in biological research has shifted to functional and structural characterization of the proteins encoded by these genomes. Efforts are being made to automate and optimize the multi-stage process of three-dimensional protein structure determination. Data management is an important aspect of this automation. ZebaView, which is available at http://www-nmr.cabm.rutgers.edu/bioinformatics/ZebaView/, is a web-based tool that allows scientists to quickly access important summary information about current protein targets in the Northeast Structural Genomics Consortium. It also allows the user to access more in depth information about the targets via links to other parts of ZebaView and outside resources. ZebaView links to Primer Prim'er, allowing users to quickly create primers for two commonly used plasmid systems. It also minimizes target overlap with other structural genomics projects and with known protein structures by providing access to tools to search against the targets of 13 different structural genomics consortiums and all released PDB structures.