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.
Builds a protein model into an electron density map. ARP/wARP facilitates model building by initially interpreting a density map with free atoms of unknown chemical identity; all structural information for such chemically unassigned atoms is discarded. It consists of a number of tasks that are performed in an iterative fashion. Free atoms are used to obtain better electron density maps through refinement. The tool is based on the paradigm of viewing model building and refinement as one unified procedure for optimizing phase estimates.
Provides a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. CNS allows heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. CNS is the result of an international collaborative effort among several research groups.
Allows automated protein structure prediction and structure-based function annotation. I-TASSER constructs, starting from the amino acid sequence, 3D structural models by reassembling fragments excised from threading templates. I-TASSER servers provides a confidence score (C-score) to estimate the models’ global accuracy. The I-TASSER Suite pipeline was tested in community-wide structure and function prediction experiments, including CASP10 and CAMEO.
Provides a suite of methods important for the prediction of protein structural and functional features. predictProtein is a web server that incorporates over 30 tools. This software searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. It can help when little is known about the protein in question. For medium-to-high throughput analyses, downloadable software packages and the PredictProtein Machine Image (PPMI) are available.
Predicts different sets of structural protein properties. SPIDER is an iterative deep-learning neural network. It obtains secondary structure, torsion angles, Cα−atom based angles and dihedral angles, and solvent accessible surface area. It utilises both local and nonlocal structural information in iterations. At each iteration, SPIDER employs a deep-learning neural network to predict a structural property based on structural properties predicted in the previous iteration.
Predicts oligomerization, functional sites, and conformational changes in transmembrane proteins. EVfold_membrane applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. The method predicts the structures of 11 transmembrane proteins of unknown structure, including six pharmacological targets. It appears to achieve a useful level of accuracy.
Offers a component-based architecture that allows users to add new functionality in the form of plug-in modules. geWorkbench includes many computational resources permitting to delete many steps that require programming skills. It simplifies the utilization of multi-module analysis pipelines. The tool’s modules consist of wrapped versions of pre-existing third-party software tools.
Combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model generation, model assessment, and model refinement. The MULTICOM protein structure prediction pipeline stands ready to meet the needs of the research community and is accessible via a web service. The method uses a multi-level combination technique to combine multiple protein structure templates and sources of structural information to generate models and then employs a number of model refinement and selection tools to return the best possible predicted structure. The MULTICOM system is capable of using both template-based and template-free modeling to handle the full spectrum of protein modeling and generate predictions for all protein structure prediction tasks from the relatively easy to difficult.
Measures electron density via a solution scattering data. DENSS is based on an iterative structure factor retrieval algorithm to rebuild the object density from the low-information limiting case of biological small-angle scattering. This software can also reconstruct complex shapes including several different particle densities without modeling. It avoids assumptions implicit to existing modeling algorithms that restrains the resolution given by envelope reconstructions.
Allows users to determine quasi-atomic-resolution structures of molecular machines. M3 employs complementary and orthogonal experimental information such as interatomic distances and molecular shapes. It is able to conserve description of physical forces at the atomic level. This tool can rearrange structures at the atomic level and returns an account on the adequacy of the input data.
Predicts 3D structure of a protein sequence. Phyre is a web application that investigates known homologues, builds a hidden Markov model (HMM) of the targeted sequence based on the detected homologues and scans it against a database of HMMs of known protein structures. It also provides advanced features such as a batch submission of a large number of protein sequences for modelling or Phyre Investigator, that allows users to analyze model quality, function and effects of mutations.
A protein structure prediction server excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model: P-value for the relative global quality, GDT (global distance test) and uGDT (un-normalized GDT) for the absolute global quality, and RMSD for the absolute local quality of each residue in the model.
An automatic protein structure prediction server. (PS)2 uses an effective consensus strategy both in template selection, which combines PSI-BLAST and IMPALA. The method uses a new substitution matrix, S2A2, that combines both sequence and secondary structure information for the detection of homologous proteins with remote similarity and the target-template alignment. The final three-dimensional structure is built using the modeling package MODELLER.
An independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance.
Allows prediction of protein structure. FRAGFOLD can generate compact structures with significant similarity to the experimentally determined structures even for proteins with entirely novel folds. Methods such as FRAGFOLD attempt to narrow the search of conformational space by preselecting structural fragments from a library of known protein structures. The original software was used in the CASP2 experiment in 1996.
Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer library, a simple energy function based on the library rotamer frequencies and a purely repulsive steric energy term, and a graph decomposition to solve the combinatorial packing problem. It calculates all the required energies and performs combinatorial optimization after which for each residue one of its rotamers will be marked as optimal.
Models side-chain conformation. OPUS-Rota uses simulated annealing by heat bath Monte Carlo as a sampling method, which is able to rapidly identify near-native conformations when combined with neighbor list techniques and efficient energy updates. It was benchmarked with 65 high-resolution X-ray structures used in the literature. The tool outperforms other related methods in terms of combined speed and accuracy.
Provides access to a variety of public and in-house bioinformatics tools. The MPI Bioinformatics Toolkit integrates a selected set of most useful methods for the analysis of protein sequences and structures. It offers more of 50 interconnected tools, so that the results of one tool can be forwarded to other tools. It also includes a useful platform for teaching bioinformatic enquiry to students in the life sciences.
Employs a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy to investigate allosterism in biological systems. WebPSN allows the user to easily setup the calculation, perform post-processing analyses and both visualize and download numerical and 3D representations of the output. Speed and accuracy make this server suitable to investigate structural communication, including allosterism, in large sets of bio-macromolecular systems.
Predicts the tertiary and secondary structure of a protein, given its amino acid sequence. Protinfo enables users to submit a protein sequence and to request a prediction of the three dimensional (tertiary) structure based on comparative modeling, fold generation and de novo methods developed by the authors. In addition, users can submit NMR chemical shift data and request protein secondary structure assignment that is based on using neural networks to combine the chemical shifts with secondary structure predictions. It serves as a complement to Bioverse framework.
Provides server for the ab initio and consensus-based prediction of protein structure. CABS-fold is a web application for protein structure, including de novo, modeling and comparative modeling using one or more structural analogs. It can also be used to predict protein loops. It operates in two modes: consensus modeling (based on structural templates) and de novo modeling (based only on sequence).
Allows high-throughput protein surface comparison, analysis, and visualization. 3D-SURFER is a web-based platform that compares the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three. The software provides two options for protein surface representation: from all surface atoms or using only backbone atoms. Users can additionally specify two types of filters: a CATH and a length filter.
Provides a web service for interactive validation and correction of Asn/Gln amide rotamers. NQ-Flipper operates in three steps: (i) a protein coordinate file is uploaded and scores based on potentials of mean force are computed, (ii) the results are displayed in a table where incorrect Asn/Gln rotamers are marked and the respective structure is shown in an interactive 3D Java applet and (iii) a coordinate file with corrected atom positions is produced.
Develops many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases.
Deals with electron crystallographic image data and yields structural information for human aquaporin-2, aquaporin-8, and bacterial porins and transporters. IPLT can be employed for the optimization of the radius that determines the size of the integrated reflection area. It offers functions that allows users to evaluate the data quality and, if necessary, to correct mistakes.
A fine-grained structural clustering method available within the T-Coffee web server. Given a set of structurally related proteins or protein families, T-RMSD will generate a supported structural clustering. The tree is supported by accuracy estimates analog to bootstrap values in phylogenetic reconstruction. Given a set of homologous sequences with known structures, the T-RMSD is a method designed to turn the multiple sequence alignment of these sequences into a structure-based clustering. This clustering is estimated through the systematic comparison of intramolecular distances, in a way similar to the DALI algorithm.
Serves for electron microscopy (EM) maps of near atomic resolution. MAINMAST is a program that performs in constructing protein structure models from an EM density map without requiring reference structures. Moreover, this tool provides a confidence level to structure regions in a model by computing consensus regions among top scoring models.
Analyses the data resulting from crystallographic fragment screening. PanDDA is a package that comprises the characterization of a set of related crystallographic data sets of the same crystal form, the identification of (binding) events, and the subtraction of ground state density to reveal clear density for events. This method is applicable and effective at any resolution, though at lower resolutions, as maps become less precise, higher occupancies of changed states will in general be required for them to be detected by Z-score.
Provides automated structure prediction and analysis tools to infer protein structural information from genomic data. Robetta uses a fully automated implementation of the Rosetta software package for protein structure prediction. The software parses input sequences into domains and builds models for domains with sequence homology to proteins of known structure using comparative modeling, and models for domains lacking such homology.
Offers a platform for determining protein structural features and tertiary structures. SCRATCH is a web application including ten modules for determining three and eight class: (1) secondary structure, (2) relative solvent accessibility, (3) domain boundaries, (4) disordered regions, (5) disulfide bridges, (6) the effect of single amino acid mutation on stability, (7) residue-residue contact maps, and (8) tertiary structures as well as contacts with other residues compared to average.
Calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input. It can be applied to newly determined experimental protein structures or theoretical models. Many membrane-associated proteins from the PDB have already been pre-calculated and can be found in the OPM database.
Predicts protein 3D structure by using single template homology model. CPHmodels was created to make a front-end that was easy to understand for users without any prior knowledge of homology modelling. It provides a result that is as accurate as possible. The tool is based on an optimized alignment scoring function and employs a double-sided Z-score to rank individual template hits. One of its major feature is the speed: for most queries the response time of the server is inferior to 20 minutes.
This technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The web server is designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables).
A comparative modeling web-server for protein structure modelling closely connected to ModBase. ModWeb accepts one or many sequences in the FASTA format and calculates their models using ModPipe based on the best available templates from the Protein Data Bank (PDB). Alternatively, ModWeb also accepts a protein structure as input and calculates models for all identifiable sequence homologs in the UniProt database. The latter mode is a useful tool for structural genomics efforts to assess the impact of a newly determined protein structure on the modeling of sequences of unknown structure. It is also used to identify new members of sequence superfamilies with at least one member of known structure. The results of ModWeb calculations are available through the ModBase interface as private datasets protected with passwords.
Assists users in reconstruction of protein backbone. SABBAC is an online tool that relies on an approach to fragment selection and assembly. It uses the encoding of the alpha-carbon trace using a hidden Markov model derived structural alphabet. It selects at each position in the structure a small set of candidates among a complete set of over 150 candidate fragments describing all the letters of the structural alphabet.
A web server predicting structure property of a protein sequence without using any templates. RaptorX-Property outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels.
Allows users to clean PDB files. KINARI-Curation is a suite of tools that lists, for a given PDB file, the models, chains, ligands, water molecules and more, included into this file. It also permits to retain desired chains and ligands and excludes data users are not interested in, such as water molecules. The software is available in “Quick-start” and “Advanced Users” mode.
Allows users to study amino acid sequence. BetaSCPWeb permits users to choose rotamers from three different rotamer libraries: the most recent backbone-dependent one in addition to the earlier backbone-independent and backbone-dependent libraries. It displays results visually and in text form. It also computes two versions of the protein structure prediction, both of which can be downloaded in PDB-format.
Generates a tertiary structure (3D model) for a given sequence-structure alignment model. AL2TS is a web server that automatically translates the alignment model into the tertiary structure (TS) format in which a given PDB entry is used as a template by which residue coordinates are assigned to corresponding residues in the 3D model.
A set of accurate tools, for analysing protein structures, based on the reliable method of Voronoi-Laguerre tessellations. The Voronoi Laguerre Delaunay Protein web server (VLDPws) computes the Laguerre tessellation on a whole given system first embedded in solvent. Through this fine description, VLDPws gives the following data: (i) Amino acid volumes evaluated with high precision, as confirmed by good correlations with experimental data. (ii) A novel definition of inter-residue contacts within the given protein. (iii) A measure of the residue exposure to solvent that significantly improves the standard notion of accessibility in some cases.
Facilitates the process of homology-based structural modeling. AS2TS is a protein structure modeling and analysis system which, for a given sequence of amino acids, performs a quick search for the closest Protein Data Bank (PDB) homologs that can be used for 3D protein structure modeling. The software has been used in several collaborative biological research projects.
Allows users to automatically annotate structural models. 3DBIONOTES authorizes users to: (i) expose the macromolecular structure submitted or queried by users; (ii) show the biomedical and biochemical data gathered from different sources; (iii) obtain the alignment between the selected UniProt sequence and the active chain of the structural model. However, the tool was only available for structures already released in structural databases.
Provides a comparative modeling tool. TASSER-Lite can be apply to the large-scale comparative modeling and is mainly developed for homologous protein sequences. The search can be run from the website by uploading or pasting a sequence in FASTA format accompanied by an email address.
Offers a platform dedicated to the visualization and interpretation of cryo-electron microscopy (cryoEM) density maps and to model multi-resolution data from biophysical sources, including small-angle X-ray scattering. Situs is composed of more than 15 tools that can be combined in various ways. The application supports three multi-resolution structure types: atomic structures, volumetric density maps and SAXS bead models.
Identifies lipid accessible residues from a protein structure. ROSIE employs a 2D concave hull algorithm on a point cloud onto the plane of the membrane. It can be applied to both α-helical and β-barrel membrane proteins of any architecture. This tool can be used in score function derivation, development of sequence-based predictors and structural modelling problems. It is a web implementation of the Rosetta software suite.
An accurate and sensitive superfamily discrimination, combining information from both sequence and structure to produce highly accurate domain alignments. The method employs the same underlying threading algorithm as pGenTHREADER, however it aligns sequences to a domain-based template library rather than a chain-based template library. The use of smaller regions of structure for templates means that different features of the alignments are required for optimal scoring. The final prediction score results from an SVM trained on a combination of 5 different feature inputs; template coverage, alignment score, template length, solvation and pairwise potentials.