Predicts magnitude and orientation of the steric component of a molecular alignment tensor. PALES uses the molecule’s three-dimensional (3D) shape to make its prediction. It is not limited to nearly neutral alignment media and can be applied to proteins, nucleic acids and oligosaccharides. The tool can be employed to verify the correctness of derived structures and to evaluate multiple-conformer models for flexible proteins.
Provides a complete software environment for bio nuclear magnetic resonance (NMR) data. NMRbox was developed to simplify discovery and use of NMR software. It also permits users to facilitate software development, deployment, and support. This server also complements BioMagResBank (BMRB), the international data repository for biomolecular NMR data, by simplifying and enriching depositions. It finally provides multiple tools for achieving reproducibility of biomolecular NMR studies.
Builds on orientational principles to allow the efficient interactive calculation and analysis of residual dipolar couplings (RDCs). REDCAT provides a user-friendly program with a graphical-user-interface permitting interaction that can be used for automated data analysis sessions. It includes combined analyses, inclusion of a flexible selection mechanism, imports/exports functions and improvement of the core computational engine.
Automates the elimination of noise peaks. Filt Robot employs convolutional neural networks (CNN) to recognize peaks for obtaining nuclear magnetic resonance (NMR) signal assignments and 3D structures. It can provide quality factors for the identified peaks. This tool finds the maximal data point in a square for 2D or cubic for 3D sub-matrix to retrieve peak positions. It uses quadratic interpolation over the closest three points in each dimension.
Allows users to proceed file conversions from 1D nuclear magnetic resonance spectroscopy (NMR) raw formats to nmrML. nmrMLconvert is a software available both as a web application and as a standalone program and includes a comprehensive JAVA-based converter. It accepts Bruker (TOPSPIN, X-WINNMR), Variant/Agilent (VNMRJ) and Jeol (JDF, DELTA) format to be performed from a compiled archive.
Permits to evaluate and compare macromolecular structures. MOLMOL generates high-quality pictures for documentation or publication, such as ribbon presentations and other schematic, simplified views of complex macromolecular structures. It evaluates the torsion angles of the polypeptide backbone. The tool can determine the principal axes of the global molecular shapes and calculates the corresponding radii of gyration.
Provides a suite for trans-omics approaches. ECOMICS is composed of four components: (i) E-class, for taxonomic classification of prokaryotic and eukaryotic DNA sequences, (ii) FT2B to process nuclear magnetic resonance (NMR) spectra for downstream chemical analyses, (iii) Bm-Char which perform an assignment of specific compounds in lignocellulose, and (iv) HetMap to identify and visualize heterogeneous data and correlation matrices.
Allows users to handle multidimensional nuclear magnetic resonance (NMR) data. Nmrglue is a module whose main functions are reading, writing, and interacting with spectral data from multiple commons formats: Bruker, Nmrpipe, Sparky ,Varian/Agilent, Simpson, Rowland. Moreover, the software also includes several common functions for processing the submitted data such as apodization, spectral shifting, or baseline smoothing and flattening. Besides, additional data formats can be implemented.
Allows users to realize proton beam calculations. BGware is a suite of program offering users several types of functions. It includes: (1) BPW; (2) CPO2; (3) FITSCAN; (4) LAMINATE; (5) LOOKUP; (6) NEU; and (7) SCANFOR.
Clusters an ensemble of nuclear magnetic resonance (NMR)-derived protein structures into conformationally-related subfamilies. NMRCORE can serve for the definition of the core atoms and local structural domains (LSDs) in ensembles of homology models. It employs a list of the variances in individual dihedral angles across the ensemble to fix the core. This tool is able to characterize the rigid bodies which comprise the core.
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