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Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications. Molekel: MM XRD: Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13 ...
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Protein structure alignment tools: tools like PyMOL and UCSF Chimera enable the visualization of sequence alignments in the context of protein structures. By superimposing aligned sequences onto protein structures , researchers can analyze the spatial arrangement of conserved residues and functional domains.
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
University of Washington and The Baker Labs; structure prediction, protein folding Proprietary, commercial or gratis fold.it download page Archived 2011-04-04 at the Wayback Machine: FoldX: I Yes Yes No No No No No No Energy calculations, protein design Proprietary, commercial or gratis CRG: GROMACS: No No Yes Yes No [2] Yes I Yes [3] Yes High ...
PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The Py part of the software's name refers to the program having been written in the programming language ...
UTOPIA (User-friendly Tools for Operating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects.
Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores: Protein: Both: D. Chivian & D. Baker [23] 2003 LALIGN Multiple, non-overlapping, local similarity (same algorithm as SIM) Both: Local non-overlapping: W. Pearson: 1991 ...