See this presentation, Protein structure analysis

New paper by deep mind Alpha Fold!

http://www.predictioncenter.org/index.cgi

Linguistic hypothesis in protein structure prediction (proteins are built out of building blocks, recursively). The basic idea is as follows: there is evidence that today’s proteins emerged out of an ancient peptidic soup, one that may have left its mark on the evolutionary record. I.e., the proteins we see today may in some sense be formed out of primordial peptides. As proteins grew in size and complexity, it would have been advantageous to reuse existing components, to build bigger proteins from existing protein parts. We already know this is true on the level of protein domains, in that larger proteins are often comprised from chaining together smaller globular domains. But the phenomenon of reuse may go further, where even smaller protein fragments (handful of residues to dozens) may reflect an underlying evolutionary pressure to reuse working parts, fragments that fold in tried-and-tested ways (from the perspective of evolution.) If this is the case, then the space of naturally occurring proteins may occupy a very special “manifold”, one that exhibits a hierarchical organization spanning small fragments to entire domains.

Two main methods:

• Template-based methods. Based on finding homologous sequences (sequences which are similar/evolutionarily related).
• Template-free methods. Based on empirically determined potentials, and using some clever stochastic search. Also, physics-based predictions (but these don't seem to work well yet, due to inaccuracies in our potentials..)

source: http://www.proteinmodelportal.org/?pid=101

See Protein folding

How to use BLAST, clustal, MODELLER, for homology modelling

Nice online software: Swissmodel info, other one. Another nice one: Phyre2 paper

Loop modelling algo: Poing

https://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software

http://www.proteinmodelportal.org/?pid=modelling_interactive

See also here: http://www.dtc.ox.ac.uk/people/11/oliveiras/miniCASP/miniCASP2.html