ProteinTools: a toolkit to analyze protein structures (original) (raw)
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3Drefine: an interactive web server for efficient protein structure refinement
Nucleic acids research, 2016
3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through variou...
Journal of Structural and Functional Genomics, 2011
The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology. Protein Model Portal Theoretical models http://www.proteinmodelportal.org PSI Technology Portal Technology reports http://technology.lbl.gov/portal/home PSI Publications Portal PSI publications http://olenka.med.virginia.edu/psi/ BioSync X-ray crystallography methods http://biosync.sbkb.org Community-Nominated Target proposal system Community requests for protein structures http://cnt.sbkb.org/CNT
BioInfo3D: a suite of tools for structural bioinformatics
Nucleic Acids Research, 2004
Here, we describe BioInfo3D, a suite of freely available web services for protein structural analysis. The FlexProt method performs flexible structural alignment of protein molecules. FlexProt simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. It does not require an a priori knowledge of the flexible hinge regions. MultiProt and MASS perform simultaneous comparison of multiple protein structures. PatchDock performs prediction of protein-protein and protein-small molecule interactions. The input to all services is either protein PDB codes or protein structures uploaded to the server. All the services areavailable at
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
Nucleic acids research, 2008
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane b-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structurebased mapping, hidden Markov models, multicomponent neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 Å RMSD). The average PROTEUS2 prediction takes »3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http:// wishart.biology.ualberta.ca/proteus2.
WIWS: a protein structure bioinformatics Web service collection
2010
The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.
ProteinDBS v2.0: a web server for global and local protein structure search
Nucleic Acids Research, 2010
ProteinDBS v2.0 is a web server designed for efficient and accurate comparisons and searches of structurally similar proteins from a large-scale database. It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches of protein structures or substructures. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison. The experimental results show that our system is able to return results of global comparisons in seconds from a complete Protein Data Bank (PDB) database of 152 959 protein chains and that it takes much less time to complete local comparisons from a non-redundant database of 3276 proteins than other accurate comparison methods. ProteinDBS v2.0 supports query by PDB protein ID and by new structures uploaded by users. To our knowledge, this is the only search engine that can simultaneously support global and local comparisons. ProteinDBS v2.0 is a useful tool to investigate functional or evolutional relationships among proteins. Moreover, the common substructures identified by local comparison can be potentially used to assist the human curation process in discovering new domains or folds from the ever-growing protein structure databases. The system is hosted at
HARMONY: a server for the assessment of protein structures
2006
Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (f,c) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY
PSSweb: protein structural statistics web server
Nucleic acids research, 2016
With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An interactive report is generated, containing a summary of the results, tables, figures and 3D visualization of superposed structures. The server is available at http://pssweb.org.
Nucleic Acids Research, 2014
The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein structures, PRISM will provide a structural model of their complex if a matching template interface is available. Users can download the complex structure, retrieve the interface residues and visualize the complex model. The PRISM web server is user friendly, free and open to all users at http: //cosbi.ku.edu.tr/prism.
Protein Peeling 2: a web server to convert protein structures into series of protein units
Nucleic Acids Research, 2006
Protein Peeling 2 (PP2) is a web server for the automatic identification of Protein Units (PUs) given the 3D coordinates of a protein. PUs are an intermediate level of protein structure description between protein domains and secondary structures. It is a new tool to better understand and analyze the organization of protein structures. PP2 only uses the matrices of protein contact probabilities and cut the protein structures optimally using Matthews's coefficient correlation. An index assesses the compactness quality of each PU. Results are given both textually and graphically using JMol and PyMol softwares. The server can be accessed from http://www.ebgm.jussieu.fr/\~gelly/index.html.