ESyPred3D is an automated
homology modeling program. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three-dimensional structure is built using the modeling package
MODELLER.
Method
To perform homology modeling, the ESyPred3D program first searches for a template (a similar sequence of known structure), before aligning the query and template sequences. EsyPred3D then build the 3D models using the alignment and the template structure, before assessing the final 3D model.
The query and the template sequences are aligned using a consensus alignment method.
Different multiple sequence alignments are built using different alignment programs on two sets of sequences including the query and the template sequence.
The consensus method uses a
neural network
A neural network is a network or circuit of biological neurons, or, in a modern sense, an artificial neural network, composed of artificial neurons or nodes. Thus, a neural network is either a biological neural network, made up of biological ...
to find the best aligned residues and analyzing all possible combinations using a dead end elimination algorithm.
The final 3D model is built from the target-template alignment and the 3D structure of the template using
MODELLER. MODELLER is also used to build the missing loops.
See also
*
List of protein structure prediction software
This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ''ab initio'' methods, secondary structure prediction, and transmembrane ...
*
Protein structure prediction
*
Homology modeling
References
{{reflist
External links
ESyPred3D web server
Molecular modelling software