| Version | MAJ | CaliFlopp | | |
| 3.0 | 2010-08-03 | Download | Doc |
CaliFloPP is a software that calculates flows of particles between pairs of polygons, when given a so-called individual dispersal function. The individual dispersal function describes the particle dispersion between pairs of points, and CaliFloPP deduces the total flows between pairs of polygons.
Remarque | Run Unix # califlopp -i polygons-filename [-p parameters-filename] [-r result-filename] | Run Web # |
CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas, techniques and practice.
Remarque | Run Unix # ccp4i | Run Web # |
Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.
Remarque Citing Coot and Friends
If have found this software to be useful, you are requested (if appropriate) to cite:
"Features and Development of Coot" P Emsley, B Lohkamp, W Scott, and
K Cowtan Acta Cryst. (2010). D66, 486-501 Acta Crystallographica Section
D-Biological Crystallography 66: 486-501
MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. Short description and demo of its three main applications are given below. Navigation portlet on the left has links to downloads, screenshots, documentation section of this website where you can find more information about MGLTools. Please visit MGL Bugzilla to submit a bug report or to request a new feature.
Remarque | Run Unix # pmv, adt, vision | Run Web # |
PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.
Remarque Citing PHENIX:
PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).| Run Unix # phenix | Run Web # |
| Version | MAJ | procheck | | |
| 3.5.4 | 2007-05-21 | Download | Doc |
Remarque
| Version | MAJ | psicov | | |
| 1.05 | 2012-07-26 | Download | Doc |
Accurate Contact Prediction from large protein alignments
Remarque | Run Unix # psicov [options] alnfile | Run Web # |
| Version | MAJ | TM-align | | |
| 20160521 | 2017-02-28 | Download | Doc |
TM-align is an algorithm for sequence-order independent protein structure comparisons. For two protein structures of unknown equivalence, TM-align first generates optimized residue-to-residue alignment based on structural similarity using dynamic programming iterations. An optimal superposition of the two structures, as well as the TM-score value which scales the structural similarity, will be returned. TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.2 corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 assume generally the same fold in SCOP/CATH.
Remarque | Run Unix # TMalign PDB1.pdb PDB2.pdb [Options]
| Run Web # |
