ESyPred3D
Encyclopedia
ESyPred3D is an automated Homology modeling
program. The method gets benefit of the increased alignment performances of an alignment strategy that uses neural networks. 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
.
The consensus method is using a neural network to find the best aligned residues and analyze all possible combination using a dead end elimination algorithm.
. MODELLER is also used to build the missing loops.
, CASP
and CAFASP
.
ESyPred3D is part of some meta-server: Meta-PP, Genetegrate and PredictProtein.
The ESyPred3D web server is running about 2600 predictions per month.
Homology modeling
Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...
program. The method gets benefit of the increased alignment performances of an alignment strategy that uses neural networks. 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
MODELLER
MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures . It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create...
.
Steps
The usual four steps of homology modeling are executed: (1) search for a template (similar sequence of known structure), (2) align query and template sequences, (3) build the 3D model using the last alignment and the structure of the template and (4) assess the final 3D model.Template selection
The template is the first PDB hit found by using maximum four PSI-BLAST iterations in the NCBI nr data bank.Sequence alignment
The query and the template sequences are aligned using a consensus alignment method. Different multiple sequence alignments are build using different alignment programs on two sets of sequences including the query and the template sequence.The consensus method is using a neural network to find the best aligned residues and analyze all possible combination using a dead end elimination algorithm.
Model generation and loop modeling
The final 3D model is build from the target-template alignment and the 3D structure of the template using MODELLERMODELLER
MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures . It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create...
. MODELLER is also used to build the missing loops.
Usage
ESypred3D has been evaluated in EVAEVA
Eva or EVA may refer to:* Eva , a given name for women** Eva , a list of people with the name EvaIt may also refer to:-In business and economics:* Earned Value Analysis, a measurement of project progress...
, CASP
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
and CAFASP
CAFASP
CAFASP, or the Critical Assessment of Fully Automated Structure Prediction, is a large-scale blind experiment in protein structure prediction that studies the performance of automated structure prediction webservers in homology modeling, fold recognition, and ab initio prediction of protein...
.
ESyPred3D is part of some meta-server: Meta-PP, Genetegrate and PredictProtein.
The ESyPred3D web server is running about 2600 predictions per month.
See also
- List of protein structure prediction software
- Protein structure predictionProtein structure predictionProtein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
- Homology modelingHomology modelingHomology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...