experimentally known functional features. It is also established that structure validation tools like PROCHECK [55] and WHAT IF [56] can only suggest the quality
of the models not the functionality of the modeled protein. Other methods popularly
known as ab initio designing of protein, alternate to template-based modeling, have
been discussed in other reviews [67, 68]. A comparison of efficiency of modeling
protein structure called CASP (critical assessment of methods of protein structure
prediction) provides evaluation of such programs [69]. Recently, designing of
protein structures has been successfully applied to model protein from genome
sequence using an integrated pipeline by Jayaram and co-workers [70]. However,
ensembles of model structure may provide a better docking success which has been
cited in 2010 by Novoa et al. [71].
Fig. 2 Two homology-based models have been developed for Mtb ICD using two different crystal
structures (one from E. coli and one from Sus scrofa). a Shows the modeled structure (dark gray
color) superimposed with E. coli crystal structure (green color). Model fit well with 4.6 Å RMSD
value. c Second model is developed using Sus scrofa structure (1LWD) and superimposed model
structure (white color) is shown with 1LWD (orange color). When Mtb structure published in
2013, it is found that mammalian ICD is much closure to Mtb as shown in panel (d) than E. coli
(panel b). Fold is well conserved in both models, but major differences are highlighted in clasp
region (shown in black circle)
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
121
of the models not the functionality of the modeled protein. Other methods popularly
known as ab initio designing of protein, alternate to template-based modeling, have
been discussed in other reviews [67, 68]. A comparison of efficiency of modeling
protein structure called CASP (critical assessment of methods of protein structure
prediction) provides evaluation of such programs [69]. Recently, designing of
protein structures has been successfully applied to model protein from genome
sequence using an integrated pipeline by Jayaram and co-workers [70]. However,
ensembles of model structure may provide a better docking success which has been
cited in 2010 by Novoa et al. [71].
Fig. 2 Two homology-based models have been developed for Mtb ICD using two different crystal
structures (one from E. coli and one from Sus scrofa). a Shows the modeled structure (dark gray
color) superimposed with E. coli crystal structure (green color). Model fit well with 4.6 Å RMSD
value. c Second model is developed using Sus scrofa structure (1LWD) and superimposed model
structure (white color) is shown with 1LWD (orange color). When Mtb structure published in
2013, it is found that mammalian ICD is much closure to Mtb as shown in panel (d) than E. coli
(panel b). Fold is well conserved in both models, but major differences are highlighted in clasp
region (shown in black circle)
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
121