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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 ...
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...
To view NMR structures, open the PDB file as usual; all coordinate sets will be loaded, but only one displayed by default. To view the structures in succession, as frames of a movie, click "Play" in the Tcl/Tk window. The frame rate can be set in the menu Movie > Speed. To view all the structures simultaneously, click Movie > Show all states ...
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]
As discussed before, MOE is a versatile software with main applications in 3D molecular visualization; structure-based protein-ligand design; antibody and biologics design, structure-based protein engineering; SAR and SPR visualization; ligand-based design; protein, DNA/RNA modeling; virtual screening; 3D pharmacophore screening; fragment-based discovery; structural bioinformatics; molecular ...
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 ...
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.
Swiss-model (stylized as SWISS-MODEL) is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. [1] [2] As of 2024, homology modeling is the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications.