Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PRISM: protein interactions by structural matching.

ABSTRACT: Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

SUBMITTER: Ogmen U

PROVIDER: S-EPMC1160261 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

PRISM: protein interactions by structural matching.

Ogmen Utkan U Keskin Ozlem O Aytuna A Selim AS Nussinov Ruth R Gursoy Attila A

Nucleic acids research 20050701 Web Server issue

Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results ar ...[more]

PMID: 15991339

Similar Datasets

PRISM: protein-protein interaction prediction by structural matching.

Project description:Prism (protein interactions by structural matching) is a system that employs a novel prediction algorithm for protein-protein interactions. It adopts a bottom-up approach that combines structure and sequence conservation in protein interfaces. The algorithm seeks possible binary interactions between proteins through structure similarity and evolutionary conservation of known interfaces. It is composed of a database containing protein interface structures derived from the Protein Data Bank (PDB) and predicted protein-protein interactions. It also provides related information about the proteins and an interactive protein interface viewer. In the current version, 3799 structurally nonredundant interfaces are used to predict the interactions among 6170 proteins. A substantial number of interactions are verified in two publicly available interaction databases (DIP and BIND). As the verified interactions demonstrate the suitability of our approach, unverified ones may point to undiscovered interactions. Prism can be accessed through a user-friendly website (http://prism.ccbb.ku.edu.tr) and it will be updated regularly as new protein structures become available in the PDB. Users may browse through the nonredundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of structures similar to these interfaces, or see the results of interaction predictions for a particular protein. Another service provided is the interactive prediction. This is done by running the algorithm for the user input structures.

| S-EPMC2685641 | biostudies-literature

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

Project description:Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.

| S-EPMC7384353 | biostudies-literature

PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.

Project description: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.

| S-EPMC4086120 | biostudies-literature

Triamine and Tetramine Edge-Length Matching Drives Heteroleptic Triangular and Tetragonal Prism Assembly.

Project description:Heteroleptic metal-organic capsules, which incorporate more than one type of ligand, can provide enclosed, anisotropic interior cavities for binding low-symmetry molecules of biological and industrial importance. However, the selective self-assembly of a single mixed-ligand architecture, as opposed to the numerous other possible self-assembly outcomes, remains a challenge. Here, we develop a design strategy for the subcomponent self-assembly of heteroleptic metal-organic architectures with anisotropic internal void spaces. Zn6Tet3Tri2 triangular prismatic and Zn8Tet2Tet'4 tetragonal prismatic architectures were prepared through careful matching of the side lengths of the tritopic (Tri) or tetratopic (Tet, Tet') and panels.

| S-EPMC10910536 | biostudies-literature

Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.

Project description:Structural details of protein interactions are invaluable to the understanding of cellular processes. However, the identification of interactions at atomic resolution is a continuing challenge in the systems biology era. Although the number of structurally resolved complexes in the Protein Databank increases exponentially, the complexes only cover a small portion of the known structural interactome. In this chapter, we review the PRISM system that is a protein-protein interaction (PPI) prediction tool-its rationale, principles, and applications. We further discuss its extensions to discover the effect of single residue mutations, to model large protein assemblies, to improve its performance by exploiting conformational protein ensembles, and to reconstruct large PPI networks or pathway maps.

| S-EPMC7900904 | biostudies-literature

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Project description:PriSM is a set of algorithms designed to select and match degenerate primer pairs for the amplification of viral genomes. The design of panels of hundreds of primer pairs takes just hours using this program, compared with days using a manual approach. PriSM allows for rapid in silico optimization of primers for downstream applications such as sequencing. As a validation, PriSM was used to create an amplification primer panel for human immunodeficiency virus (HIV) Clade B.The program is freely available for use at: www.broadinstitute.org/perl/seq/specialprojects/primerDesign.cgi.

| S-EPMC3018813 | biostudies-other

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

2015-02-27 | E-GEOD-56010 | biostudies-arrayexpress

Protein-RNA interactions: a structural analysis.

Project description:A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.

| S-EPMC29619 | biostudies-literature

Graphene perfect absorber of ultra-wide bandwidth based on wavelength-insensitive phase matching in prism coupling.

Project description:We proposed perfect absorbers of ultra-wide bandwidths based on prism coupling with wavelength-insensitive phase matching, which consists of three dielectric layers (Prism-Cavity-Air) with monolayer graphene embedded in the cavity layer. Due to inherent material dispersion of the dielectric layers, with the proper choice of the incidence angle and the cavity thickness, the proposed perfect absorbers can satisfy the phase matching condition over a wide wavelength range, inducing enormous enhancement of the absorption bandwidth. The requirement on the material dispersions of the prism and the cavity layer for the wavelength-insensitive phase matching over a wavelength range of the interest has been derived, and it has been demonstrated that the various kinds of materials can meet the requirement. Our theoretical investigation with the transfer matrix method (TMM) has revealed that a 99% absorption bandwidth of ~300?nm with perfect absorption at ? ?=?1.51 ?m can be achieved when BK7 and PDMS are used as the prism and the cavity layer, respectively, which is ~7 times wider than the conceptual design based on the non-dispersive materials. The full width at half maximum of our designed perfect absorber is larger than 1.5 ?m.

| S-EPMC6700108 | biostudies-literature

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

2015-02-27 | GSE56010 | GEO