2019---2020-partage

For exchanging material and doc

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Bibliography (Biblio)

For profile-profile alignments and (remote) homology detection

ORION: fold recognition method based on profile-profile alignments

scoringProfiles: methods to score profile-profile alignments

HHsearch: remote homology detection using profiles (defined from hidden Markov models, not from PSSM!)

CLADE: remote homology detection using a multi-profile strategy

For evaluating the quality of a 3D model

DOPE: "historical" statistical potential for evaluating the quality of 3D models (does not perform very well but is a good start)

Rosetta: a reference function for estimating the energy of a 3D protein conformation (be aware it's all-atom!)

SBROD: coarse-grained statistical potential to evaluate 3D models quality (can be applied to Calpha-only or backbone-only structures, recently performed well in CASP13, can be completely re-trained!)

For structural annotations (secondary structure, solvent accessibility, contacts... predicted from sequence)

ReviewSA: book chapter reviewing methods to predict secondary structure, solvent accessibility, torsional angles and contact maps, from sequenc information)

CCMPRED: method to predict protein-protein contact by extracting coevolution signals (co-occurring patterns of mutations across sequences)

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