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PHENIX / Python-based Hierarchical ENvironment for Integrated Xtallography
Allows automated determination of molecular structures using X-ray crystallography and other methods. PHENIX is a software suite which provides a range of tools for the analysis, validation and manipulation of X-ray diffraction data. The software was developed as a highly-automated system that can arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data.
Allows checking of the stereochemical quality of a protein structure. PROCHECK is a suite of programs that uses stereochemical considerations alone, both to provide an overall assessment of the stereochemistry of a given structure and to highlight regions that may need further investigation. The software can be useful for the solution of new structures, assessment of existing structures and model building of unknown structures. PROCHECK-NMR is included in the suite and allows analysis of ensembles of protein structures.
A standalone suite of programs to plot the distribution of residues embedded at a globular protein interior in the Complementarity Plots. The complementarity plot (CP) is based on packing and electrostatics of amino acid residues buried within globular proteins and is a sensitive indicator of the harmony or disharmony of interior residues with regard to short and long range forces sustaining the native fold. As a structure validation tool, it was reported to be effective in detecting erroneous side-chain torsions in obsoleted structures. The application of CP in protein homology modeling and protein design was also demonstrated. The tool was further extended to the validation of Protein-Protein Interfaces (SARAMAint).
SIRAH tools / Southamerica Initiative for a Rapid and Accurate Hamiltonian tools
A toolkit for mapping, backmapping and visualization of coarse-grained (CG) models. SIRAH tools provides a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field.
ProSA-web / Protein Structure Analysis-web
A tool for experimental structure determinations and modelling studies. ProSA has a large user base and is employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. ProSA is a tool used to check 3D models of proteins structures for potential errors. The web-based version of ProSA encourages structure depositors to validate their structures before they are submitted to Protein Data Bank (PDB) and to use the tool in early stages of structure determination and refinement.
SUPRB / Suboptimal alignment-based PRoBabilistic residue
Provides a template-based structure prediction method using suboptimal alignment information. SUPRB considers interaction pairs in a probabilistic fashion by counting residue interactions in suboptimal alignments with the aim to improve how to handle a two-body amino acid contact potential in template-based structure prediction. The algorithm evaluates the suitability of a query sequence to template structures by making use of a sequence-structure compatibility score which combines five different scoring terms (a sequence profile score, a secondary structure matching score, a solvent accessibility score, a main-chain angle propensity, and an amino acid contact potential).
Simplifies the crystal structure-determination process. Mumbo helps to identify the correct orientation of the side chains during refinement. It can resolve the side-chain positioning problem in general and is able to reproduce for a number of test cases the orientations of the side chains observed in a crystal structure when starting solely from the correct backbone trace. The tool is able to very quickly identify the correct side-chain orientations, not only at high resolution but also in the case where only data to low resolution are available.
Provides a framework for fitting conformations on a fixed backbone into electron density. Current Fitmunk applications can assist in protein model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density.
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