3rd party useful tools
- Situs Very useful program package for the modeling of atomic resolution structures into low-resolution density map s e.g. from electron microscopy, tomography, or small angle X-ray scattering. It includes many useful tools
- EMDB Macromolecule structure database includes EM-Search tool for Electron Microscopy Maps
- Spider The "classic" EM image processing system.
- EMAN It's a software for single particle analysis and electron micrograph analysis, but includes many usefull tools for docking such as PDB2MRC nad PROC3D.
- Bsoft Other EM package with tools.
- em2em Program to convert images from/to formats used in the "electron microscopical community"
- mapman Other 3D map conversion tool.
- Molprobity Online structure validation tool.
- pdb2pqr Tool for preparing structures, assigning charge and radius parameters from a variety of force fields, etc.
- Jackal Includes profix tool a nice tool for fix pdbs.
- SABBAC Online server to generate backbone N and C atoms from Cα structures.
- Viper VIRUS structures data-base.
- Johnson Lab Interesting web with many Viral structures from both Cryo-EM and X-ray crystallography.
- MolMovDB Molecular Motions Database.
Other flexible fitting programs
- NMFF Normal Mode Flexible Fitting.
- NORMA Normal mode fitting of crystal structures into EM densities using URO and NMA.
- Flex-EM Either Conjugate Gradients or Molecular Dynamics based fitting and refinement method (runs under MODELLER).
- COLORES A general purpose, multi-processor capable rigid-body search tool, suitable for situations where not all density is accounted for by the atomic structure. This tool performs a full exhaustive search in 6D search space (3 translational and 3 rotational degrees of freedom). The translational search is FFT-accelerated and the program supports the use of a Laplacian-style filter (can be turned off) that drastically increases the fitting contrast at medium to low resolution.
- MDFF The molecular dynamics flexible fitting (MDFF) method is based on a molecular dynamics (MD) simulation where the driving forces to flexible fit the atomic structures into density maps are just external forces proportional to the gradient of the map.
- YUP.SCX The Yup.scx program fits a molecular structure into a density map using a molecular model based on atoms connected by a Gaussian Network. The density map is represented by a cloud of attractive holes, each hole is fixed in space and attracts all the atoms that are within an adjustable distance. The fitting is accomplished by finding the minimum of the combined Gaussian Network and attractive hole energy functions.
- MDFIT The MDfit method starts defining the initial conformation as the lowest energy configuration. The flexible fitting driving force is a cross-correlation based potential term that is superposed to all-atom structure-based potentials.