Structural Unemployment

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

pySTEP or Python Strongly Typed gEnetic Programming: A light Genetic Programming API that allows the user to easily evolve populations of trees with precise grammatical and structural constraints.

Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.


Platforms: Windows, Mac, Linux

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.


Platforms: Windows, Mac, Linux

Sometimes you want to work more with the form of an XML document than with the structural information it contains. For instance if you wanted to change a bunch of entity references or element names. Also, sometimes you have slightly incorrect XML that a traditional parser will choke on. In that...


Platforms: Windows, Mac, *nix, Python, BSD Solaris

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and...


Platforms: Windows, Mac, *nix, Python, BSD Solaris

This model demonstrates how to implement a coupled structural-aerodynamic problem.The wing, otherwise rigid, is allowed to pitch and plunge. The motion of the wing is defined using SimMechanics blocks. The aerodynamic model is a simple, quasi-steady formulation.Dynamic pressure is manipulated by...


Platforms: Matlab

Engineers are often interested in obtaining optimal topologies, i.e., optimal conceptual designs, for various structural problems. The attached Matlab code generates such optimal topologies in about 199 lines of Matlab code. Two structural problems are 'hard-coded' as illustrative examples....


Platforms: Matlab

CleverCSS is a small markup language for CSS inspired by Python that can be used to build a style sheet in a clean and structured way. In many ways it's cleaner and more powerful than CSS2 is.The most obvious difference to CSS is the syntax: it is indentation based and not flat. While this is...


Platforms: Python

CMView is an intervative contact map visualization and analysis tool. The current version is 0.9.6 Please send feedback to stehr ?*A*t molgen.mpg.de Main features: * Combined contact map and 3D structure view (using PyMol) * Various im- and export options: PDB files, Online PDB, Image...


Platforms: Mac

ProDy is a Python package designed for protein structural dynamics analysis. ProDy is developed by Ahmet Bakan and licensed under the GPLv3. New features and functions are constantly being added to ProDy. The following are the main features that are present and working fine: Protein structure...


Platforms: Mac

QPDF is a command-line program that does structural, content-preserving transformations on PDF files. It could have been called something like pdf-to-pdf. It also provides many useful capabilities to developers of PDF-producing software or for people who just want to look at the innards of a PDF...


Platforms: *nix

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies This tool aims to identifying structural variations with both clustering and...


Platforms: *nix

igraph is a free software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community...


Platforms: *nix

ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.


Platforms: *nix

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in computational structural biology to facilitate and standardize the development of molecular modeling, design and analysis tools.


Platforms: *nix

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures. Features . Protein Structure Quality...


Platforms: *nix

The NSS module is a fork from the nss_ldap package by PADL Software Pty Ltd.. This fork was done to implement some structural design changes. These changes were needed because there are some issues with the original design. See the documentation section for more details. The biggest advantages of...


Platforms: *nix

ProDy is a free and open-source Python package for analyzing protein structural dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics. The input for ProDy is the atomic coordinates of...


Platforms: *nix

VTracer is a Verilog Testbench developer aid. Contains well documented Verilog-Perl co-simulation environment (TCP sockets based), structural Verilog parser, demo Testbenches.


Platforms: *nix