From: Comparative modelling of protein structure and its impact on microbial cell factories
PROGRAM | Server/Web adress | Reference |
---|---|---|
Template Selection | ||
PSI-BLAST | [20] | |
HMMER (HMM search) | [35] | |
TOPITS | http://www.embl-heidelberg.de/predictprotein/submit_adv.html | [17] |
FUGUE | [26] | |
Threader | [27] | |
3D-PSSM | [28] | |
PFAM | [25] | |
PHYLIP | [31] | |
Target-Template alignment | ||
CLUSTALW | [34] | |
HMMER (HMM align) | [35] | |
STAMP | [36] | |
CE | [37] | |
DSSP | http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html | [38] |
Model Building | ||
COMPOSER | [39] | |
SwissModel | [41] | |
3D-JIGSAW | [44] | |
MODELLER | [46] | |
Loop Modeling | ||
MODLOOP | [50] | |
ARCHDB | [51] | |
Sloop | [52] | |
Sidechain Modeling | ||
WHAT IF | [55] | |
SCWRL | [56] | |
Evaluation of the model | ||
PROCHECK | [67] | |
PROSA II | [70] | |
Biotech | Â | |
Refinement | ||
GROMOS | [74] | |
CHARMM | [75] | |
AMBER | [76] |