A collection of programs, associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. CCP4 is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. A method for experimental X-ray data analysis called AUSPEX was integrated in CCP4.
Refines macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. RELION employs an empirical Bayesian approach. It can be utilized for both simulated and experimental data. This tool estimates the accuracy of alignment of individual particles and the relative contribution of the different frequencies therein. It enables the correction of per-particle defocus variations.
Estimates small (SM) and macromolecular (MM) crystal structures by single crystal X-ray and neutron diffraction. SHELX can be used for searching for disulfides with a fixed S–S distance in the peak-search routine of the dual-space direct methods. It can be useful to construct a polyalanine trace for proteins. This tool can serve for the investigation of single isomorphous replacement with anomalous scattering (SIRAS) data in which anomalous scatterers have been introduced.
Aids crystallographic refinement at medium and higher resolutions over the past few decades. With REFMAC5, structural information may be utilized in various forms, such as secondary-structure restraints, homologous reference structures and homology models. This tool utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization.
Selects blocks following a reproducible set of conditions. Gblocks is a program that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. It provides a web server that implements important features to make its use as simple as possible without losing the functionality that it is necessary in most of the cases.
Offers users a wide range of options for Protein Data Bank (PDB) file conversion, modification and parameterization. PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. The PDB2PQR web service is driven by a modular, Python-based collection of routines, which provides considerable flexibility to the software and permits noninteractive, high-throughput usage.
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.