Eugene Krissinel

Overview of the CCP4 suite and current developments

An overview of the CCP4 software suite for macromolecular crystallography is given.

Developments in the CCP4 molecular-graphics project

Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Summary This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

The CCP4 molecular-graphics project

This new package will provide easy-to-use access to crystallographic structure solution, model building and structure analysis. It will be possible for any developer to integrate scientific software into the system.

Remediation of the protein data bank archive

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.

Stock-based detection of protein oligomeric states in jsPISA

A new version of the popular software PISA for the analysis of macromolecular interfaces and identification of biological assemblies (complexes) from macromolecular crystal structures is presented. The new web server jsPISA has a substantially improved user interface, based on modern JavaScript technologies, and also new elements of analysis: assembly stock and interaction radar. The new elements help interpretation of PISA results in difficult and ambiguous cases, for example, when the oligomeric state depends on protein concentration, or when the biologically relevant interaction is weak and cannot be easily discriminated from superficial crystal contacts. jsPISA is maintained by CCP4 at http://www.ccp4.ac.uk/pisa. There are no login requirements for using the server.

CCP4i2: the new graphical user interface to the CCP4 program suite

CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.

CCP4 web services and cloud computing developments

The Collaborative Computational Project Number 4 in Protein Crystallography (CCP4) exists to maintain, develop and provide world-class software that allows researchers to determine macromolecular structures by X-ray crystallography and other biophysical techniques. Already for 38 years, the CCP4 Software has been assembled and distributed as an integrated Suite of programs, installable on either users’ personal PCs or centralized facilities. The Suite is traditionally operated via CCP4i(2) Graphical User Interface and is available for all major Linux, Mac OSX and Windows platforms. Modern trends in computing suggest a fast-growing interest to mobile platforms and cloud solutions for data storage and operations in practically all areas. These trends are observed in both hardware (such as the appearance of Chromebook-like and tablet devices) and operating systems, which now routinely include a number of cloud services from their vendors, changing the pattern of ordinary computing. In context of crystallographic computing, cloud solutions become increasingly appealing also in view of recent advances in automated structure solution methods, which are demanding for both computing power and various databases, making them less convenient for offline setups. Yet another reason for mobile trend to persist is that the cloud model of operations simplifies software and data management for both software provider and end users. Although CCP4 invested a considerable effort into development and maintenance of its dynamic update system, keeping both software and data resources in sync proves to be a burden for many users with limited computer or Internet resources. CCP4 steps into the area of mobile computing and cloud services in 3 different ways. Firstly, it provides a set of free web services for automated structure solution. In many cases, an upload of reflection data and sequence is all what a user needs to do in order to solve their structure. Secondly, a system of cloud-based virtual machines with per-user persistent storage, access to collected data at DLS synchrotron and pre-installed CCP4 software is under development to serve computing needs of MX community in the UK. Thirdly, RESTful API is being developed, which will provide access to remote CCP4 computing on script level. Further plans include the development of native HTML5 interface for CCP4 Software, which would be useable on all mobile devices. We will discuss these developments, achieved results and future directions in middle-term perspective.

Stock-based detection of biological assemblies in PISA software

PISA (Protein Interfaces, Surfaces and Assemblies) software from CCP4 remains a popular computational tool for the prediction of biological assemblies (complexes) from macromolecular crystallography data [1]. The method is based on the estimation of the dissociation free energy of predicted complexes, and reaches 90-95% correct results for the current content of the PDB. It was found that the probability of getting wrong predictions grows exponentially with the decrease in the dissociation free energy, reaching over 50% for complexes bound as weakly as few kcal/mol [2]. Among few reasons for this behaviour [2] is the fact that oligomeric state of weakly bound complexes is expected to vary in dependence of chemical environment, in particular, protein concentration. It has been noticed in multiple use cases, that a considerable share of disagreements between predicted and measured oligomeric states belongs to situations where the relation between experimental conditions and protein’s working environment in the cell is unclear. We report further advance in PISA software, which allows a researcher to model concentration dependence of predicted oligomeric states, and by this to improve interpretation of both experiments and computations in the biologically interesting case of weakly bound macromolecular associations. The new PISA is based on the concept of assembly stock, which represents an equilibrated set of of all complexes, compatible with crystal packing. Graphical representation of concentration (or newly introduced aggregation index) profiles of stock’s components allows a user to quickly identify the most probable oligomeric state. This is vastly superior over the previous way of analysis, based on the interpretation of bare figures for dissociation free energies. Other developments include advanced graphical interface and multi-parametric interaction radar, which indicates the likelihood for interface to represent a biologically-relevant interaction.

CCP4: a resource for macromolecular crystallography

CCP4 has been serving the software needs of the protein crystallography community for more than 30 years. In this time the CCP4 Suite of software has been refined through contributions from some of the leading developers in the field of protein crystallographic software and the feedback of both expert and novice users. Today it is a highly comprehensive suite, providing tools and packages covering all aspects from data collection through to structure deposition. Here we will present details of the latest release series of the Suite, version 6.4. This release brings updates to many of the key elements in the Suite. The most obvious of these is the integration of the rolling updates mechanism. This is used to distribute timely fixes, update existing programs and introduce new functionality to users of the suite. Recent updates have seen updates to major programs such as phaser and imosflm/mosflm, and the introduction of a major overhaul of the Experimental Phasing pipeline Crank. An overview is given of the operation behind the updates and releases, including the jhbuild system, repositories and testing, the availability of nightly builds, and work towards the next major release of CCP4. This will see the integration of the CCP4MG package, along with preparations for the introduction of the long awaited CCP4i2.