Introduction to molecular visualization: Difference between revisions
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''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ||
==Representations of Molecular Models== | ==Representations of Molecular Models== | ||
===Atomic Representations=== | ===Atomic Representations=== | ||
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You can browse for molecular models at the [http://atlas.molviz.org Atlas of Macromolecules], the [http://pdb101.rcsb.org/ Molecule of the Month], or [https://web.expasy.org/spotlight/ Protein Spotlight]. | You can browse for molecular models at the [http://atlas.molviz.org Atlas of Macromolecules], the [http://pdb101.rcsb.org/ Molecule of the Month], or [https://web.expasy.org/spotlight/ Protein Spotlight]. | ||
[[How To Find A Structure]] explains an easy way to find a structure for a protein of interest, and how to choose the best one available when there is more than one. | [[How To Find A Structure]] explains an easy way to find a structure for a protein of interest, and how to choose the best one available when there is more than one. [[Empirical models]] are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are the most reliable, but one must pay attention to the [[Quality assessment for molecular models|quality of an empirical model]] since some are more reliable than others. | ||
Empirical models are available for only a small fraction of all proteins, probably <10%. When an empirical model is not available, [[AlphaFold]] has a proven track record of predicting protein structures correctly from their sequences, using artificial intelligence (AI). [[AlphaFold]] also reliably predicts the confidence of each part of a predicted structure. | Empirical models are available for only a small fraction of all proteins, probably <10%. When an empirical model is not available, [[AlphaFold]] has a proven track record of predicting protein structures correctly from their sequences, using artificial intelligence (AI). [[AlphaFold]] also reliably predicts the confidence of each part of a predicted structure. | ||
