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HOMA: HOmology Modeling Automatically
This method of homology modeling uses distances calculated from an input template structure to determine the structure of a homologous protein. The 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.

Primer Primer – Automated PCR Primer Design
Primer Prim'er ( PP ) is a PCR primer design tool that completely automates the primer design process. PP generates vector specific PCR primer sets designed to amplify and insert DNA targets into your labs vectors. PP is designed to be a teaching tool as well as a powerful tool for structural genomic efforts. PP calculates more than just the target annealing region of PCR primers. PP introduces endonuclease restriction sites into calculated primer sets. Restriction sites are embedded into target sequences when applicable and additional nucleotides are added in order to preserve frame with vector based fusions and to ensure proper endonuclease cleavage. PP is very customizable. Aside from being able to define and employ your own vectors, a variety of settings can be tailored.

AutoProc – Automated NMR data processing
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) scripts are automatically generated based on Pulse Sequence-dependent and Spectrometer-dependent information found in the AutoProc data tables. AutoProc supports both Varian & Bruker file formats and can also be used for processing GFT NMR experiments.

AutoAssign – Automated NMR Backbone Resonance Assignment
AutoAssign is an artificial intelligence package for automating the analysis of backbone resonance assignments using triple-resonance NMR spectra of proteins. Specifically, AutoAssign is a constraint-based expert system implemented in C++, Java2, and Perl programming languages and supported on SGI-IRIX, Sun-Solaris, MAC-OSX, x86-Linux, and x86_64-Linux architectures. The new AutoAssign distribution automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples. The rich graphical user interface (GUI) provides a many sets of tools for dataset conversions, assignment validations, and various graphical displays of assignment results. AutoAssign is well tested on a large number of independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~32 kD, including one fully-deuterated protein and and a dataset with reduced-dimensionality experiments. AutoAssign performs the automated analysis of assignments in only seconds on current RISC and x86 platforms.

AutoStructure/RPF: Automated Determination of Protein Structures from NMR Data
AutoStructure is a protein structure determination tool that uses uninterpreted NOESY cross peaks together with structure calculation programs like XPLOR or DYANA to generate a 3D structure of the protein that is as close to the true structure as possible. AutoStructure uses an iterative bottom-up topology-constrained approach to analyze NOE peak lists. It first builds an initial fold based on intraresidue and sequential NOESY data, together with characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unique long-range packing NOE interactions based on chemical shift matching and symmetry considerations. Unassigned NOESY cross peaks are not used in structure calculations. Additional NOESY cross peaks are iteratively assigned using intermediate structures and the knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. This protocol, in principal, resembles the methodology that an expert would utilize in manually solving a protein structure by NMR.

RPF uses a novel, rapid, and simple approach for calculating global structure quality scores. Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D, and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

PSVS – Protein Structure Validation Suite (NMR/Xray)
The protein structure validation software suite (PSVS) is used for assessment of protein structures generated from NMR or X-ray crystallographic methods. The software integrates under a single interface analyses from several widely-used structure quality evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283–291), MolProbity (Lovell et al., Proteins 2003;50:437–450), Verify3D (Luthy et al., Nature 1992;356:83–85), ProsaII (Sippl, Proteins 1993;17:355–362), the PDB validation software, and various structure-validation tools. PSVS provides standard constraint analyses, statistics on goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. The analysis provides both global and site-specific measures of protein structure quality. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures. PSVS is particularly useful in assessing protein structures determined by NMR methods, but is also valuable for assessing X-ray crystal structures or homology models.

SPINS – Standardized ProteIn NMR Storage
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.