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List of sequence alignment software; List of open-source healthcare software; List of biomedical cybernetics software; List of freeware health software; List of genetic engineering software; List of molecular graphics systems; List of systems biology modelling software; Comparison of software for molecular mechanics modeling
Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred
Ideal DNA/RNA - build an ideal DNA or RNA fragment. Find ligands - find and fit a model to any small molecule which may be bound to the macromolecule. Tools for moving existing atoms: Real space refine zone - optimize the fit of the model to the electron density, while preserving stereochemistry. Regularize zone - optimize stereochemistry.
Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...
The Staden Package was developed by Rodger Staden's group at the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England, since 1977. [2] [3] [4] The package was available free to academic users, with 2,500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development ended. [5]
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List of protein structure prediction software; List of sequence alignment software; List of gene prediction software; List of RNA structure prediction software; Comparison of software for molecular mechanics modeling; List of software for Monte Carlo molecular modeling; List of software for nanostructures modeling; Force field