Structural Biology Software Database
Structural Biology Software Database

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Category: DNA, RNA and Protein Stucture Prediction (8 entries)

A collection of tools for structure prediction of DNA, RNA and Protein.


Circles is an experimental Windows 95/98/NT program for inferring RNA secondary structure using the comparative method. It provides a user-friendly interface to Jack Tabaska maximum weight matching programs. The user can read in an alignment in FASTA, Clustal, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in standard formats.
View Application Entry for Circles


ESSA is an integrated and interactive computer tool for analysing RNA secondary structure. ESSA software is available for current UNIX workstations such as Hewlett-Packard (HP-UX 9.0 or later), Intel Linux (Kernel 2.2.5-15 or later), Silicon Graphics (IRIX 5.3 or later), Sun (Solaris 2.4 or later).
View Application Entry for ESSA


Jnet is a program using Neural Network to do Protein Secondary Structure Prediction Method
View Application Entry for Jnet


kPROT is a WWW service for structure prediction of membrane proteins, specifically designed for transmembrane proteins with multiple alpha-helical spans. It provides a prediction of the angular orientation of the segment. You submit protein sequence(s) of previously identified transmembrane segment. The server predicts the helical orientation of the segment as expected to be when embedded in a helical bundle within the membrane i.e. lipid-exposed vs. protein-buried faces of alpha-helices The Helical orientation predictions are done with the "knowledge-based Propensities for Residue Orientation in Transmembrane segments" (kPROT) energy-like scale.
View Application Entry for kPROT


mfold is a package for RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. The mfold software now runs on a variety of Unix platforms; specifically SGI Irix, Sun Solaris, Dec alpha Ultrix and on Linux. While the older interactive programs of version 2 still exist, they are now run by a variety of scripts that make for much easier handling. There is both a command line interface for mfold and an HTML interface that runs in a Unix environment but can be accessed by anyone with a web browser.
View Application Entry for mfold

Superpositional Structure Assignment (SSA)

Superpositional Structure Assignment (SSA) is a software which automates the assignment of the secondary structure of a peptide from its atomic coordinates in PDB format based on their superposition with sequences of ideal secondary structure.
View Application Entry for Superpositional Structure Assignment (SSA)

Vienna RNA Package (RNA Secondary Structure Prediction and Comparison)

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).
View Application Entry for Vienna RNA Package (RNA Secondary Structure Prediction and Comparison)

Westhof Programs

Westhof Programs is an RNA refinement and modeling package.
View Application Entry for Westhof Programs

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