Table 1.
Availability of tools for structural modeling with 3D EM maps
| Method Name | Availability (Web URL) | Description |
|---|---|---|
| Chimera | www.cgl.ucsf.edu/chimera | Visual modeling program that contains tools for EM fitting, segmentation and related features |
| Coot | www.biop.ox.ac.uk/coot | Visual macromolecular model building, model completion and validation |
| Situs/colores | situs.biomachina.org | Rigid fitting, included as part of the Situs package |
| EMFit | bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/emfit.php | Correlation-based rigid fitting |
| ADP_EM | sbg.cib.csic.es/Software/ADP_EM | Rigid and flexible fitting, optimized by using spherical harmonics to search the rotational space |
| MODELLER/Mod-EM | www.salilab.org/modeller | Mainly for comparative (homology) modeling. Mod-EM is an extension used for fitting |
| Gmfit | strcomp.protein.osaka-u.ac.jp/gmfit | Rigid fitting based on Gaussian Mixture Models |
| 3SOM | www.russelllab.org/3SOM | Rigid fitting based on surface overlap |
| MultiFit | www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.html | Rigid fitting of multiple components that adds shape-based terms |
| BCL::EM-Fit | meilerlab.org | Rigid fitting based on geometric hashing |
| Gorgon and Pathwalking | gorgon.wustl.edu | Structure modeling secondary structure prediction and fitting |
| EMatch | bioinfo3d.cs.tau.ac.il/EMatch | Fold recognition (in its initial stages) and rigid fitting |
| SSEhunter SSEbuilder Helixhunter Foldhunter |
blake.bcm.edu/emanwiki | These methods are included as part of EMAN2. Foldhunter performs rigid fitting while the other three methods deal with SSE identification |
| Rosetta/EM-Fold | meilerlab.org | Alpha-helix identification and modeling implemented as an extension in the Rosetta prediction and modeling package. |
| EM-IMO | wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:cryoEM | Homology modeling refinement using EM maps as constraints. |
| Flex-EM/RIBFIND | salilab.org/Flex-EM ribfind.ismb.lon.ac.uk |
Flex-EM is a correlation-based flexible fitting method with MD refinement. RIBFIND is an extension included in Flex-EM that helps identify rigid bodies in structures |
| MDFF | www.ks.uiuc.edu/Research/mdff | Extension to molecular dynamics to perform flexible fitting |
| DireX | www.schroderlab.org/software/direx/index.html | Flexible fitting using deformable elastic networks |
| NORMA | elnemo.org/NORMA | Flexible fitting that considers symmetry. Is uses elNémo for computing protein flexibility. |
| S-flexfit | biocomp.cnb.csic.es/Sflexfit | Flexible fitting using structural variation in superfamilies |
| FRODA | flexweb.asu.edu | Flexible fitting with constrained geometric simulations |
This table only lists programs that are available on the Internet. They are mentioned in the text.