同源建模服务器与程序总结

同源建模服务器与程序总结

参考自salilab实验室

1. 服务器（Web-servers）

Server	Description
Fugue	Sequence-structure homology recognition.
HHPred	Sensitive protein homology detection and structure prediction by HMM-HMM-comparison.
I-TASSER	Threading fragment structure reassembly.
3D-JIGSAW	Fragment assembly.
IntFOLD	Integrated Protein Structure and Function Prediction Serve.
M4T	Comparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments.
ModWeb	Comparative modeling server based on Modeller.
Phyre2	Protein homology/analogy recognition engine.
RaptorX	Remote homology detection, protein 3D modeling, binding site prediction.
Robetta	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction.
SwissModel	Local similarity/fragment assembly.

2 本地程序（Programs）

Programs	Description
Modeller	Comparative modeling by satisfaction of spacial restraints.
Rosetta@home	Distributed-computing implementation of Rosetta algorithm.
RosettaCM	Molecular modeling softward.
MolIDE	Open-source cross-platform graphical environment for homology modeling.
HHSuite	HHSearch, HHBlits, and pre-compiled databases.
I-TASSER Suite	I-TASSER Suite is a package of standalone computer programs, developed for high-resolution protein structure prediction, refinement, and structure-based function annotations.

3. 同源建模评价方法

Programs	Description
Cameo Quality Estimation	Participating Groups in the Cameo QE project.
ModEval	Estimates model quality by estimating the native overlap, and by computing scores and profile based on statistical potentials: TSVMod, zDOPE, GA341, zDOPE-Profile.
ProQ2	Support Vector machine based predictor.
Prosa 2003	Knowledge-based potentials of mean force.
QMEAN Local	Composite scoring function describing five different structural descriptors.
SwissModel Workspace	Several assessment tools to estimate the quality and structural features of protein models and template structures: Dfire, Procheck, DSSP, Promotif, Anolea, Gromos, QMEANS6.
Verify 3D	Measures the compatibility of a protein model with its sequence using a 3D profile.
What_Check	Protein verification tools.
ModFold	Model Quality Assessment Server.
ProSA-web	Protein-Structure Analysis.
Kinemage	3D Macromolecule analysis, includes Kinemage 3D graphics, Rampage for Ramachandran plot generation, MolProbity structure validation, and more.