3d protein structure tool

The Iridium dataset allows up to two heavy atoms not to be supported by electron density. We also added selection criteria like B Factor distribution to extend the criteria catalog beyond those of the three datasets. StructureProfiler was validated against the three aforementioned datasets. In the following, the most important discrepancies per dataset are briefly discussed and full results can be found in the Supplementary Section S2. Electron density maps were downloaded from PDBe Gutmanas et al.

As a final application, we are profiling the PDB downloaded on , maximum resolution of 3. The PDB Ids annotated with ligand identifiers currently passing the combined filter criteria are given in the Supplementary Material. All ligands in the Astex set need to fulfill the Lipinski Rule of five.

We detected in G , 1ygc 8 Lipinski donors and 11 acceptors Supplementary Fig. Additional information can be found in Supplementary Section S2. Twelve ligands with more than two atoms inconsistently supported by electron density in regards to EDIA i were found Supplementary Fig. In the case of Alpha 2, 3 -Sialyllactose in chain C, asparagine E 7 is only 2. Additionally, three active sites have atoms with an occupancy below 1 Supplementary Section S2. One of these residues is in close proximity to the ligand and does not meet the requirements of the Iridium HT set.

We also found EDIA m violations. This e. Discussion of the bond length and angle violations can be found in Supplementary Section S2. We also controlled the Platinum set with the combined criteria set detecting 19 intermolecular clashes between active site and ligand among others. This shows that datasets applicable for one use case may not be fitting for other ones. StructureProfiler is available as part of our Proteins Plus web service.

One of the four configurations astex-like, iridium-like, platinum-like and combined can be selected. Failed tests and substructures with at least one failed test are marked in red.

The usage description of the customizable command line tool can be found in the Supplementary Section S1. StructureProfiler assembles the currently relevant structure quality criteria catalog in a configurable standalone, easy-to-use tool, which is also available on the web.

It allows rapid screening of inhouse data as well as easy repeated screenings of public databases. Due to the use of EDIA, it reduces human curation to a minimum in terms of electron density support control thus solving the up to now existing bottleneck in dataset curation.

StructureProfiler serves as the next step towards the creation of large high quality datasets for docking, 3D-QSAR and the many new machine-learning-based applications appearing right now. Nucleic Acids Res. Google Scholar. Friedrich N. Goto J. Gutmanas A. Hartshorn M. Jones T. Acta Crystallographica Section A , 47 , — Lipinski C. Drug Delivery Rev. Meyder A. Tickle I. Acta Crystallographica Section D , 68 , — Warren G.

Drug Discov. Today , 17 , — Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Search Menu. Article Navigation.

Close mobile search navigation Article Navigation. Volume Article Contents Abstract. StructureProfiler: an all-in-one tool for 3D protein structure profiling. Agnes Meyder , Agnes Meyder. Oxford Academic. Stefanie Kampen. All Links on 3-D Structure Analysis. Structure Annotation Tools. SAS is a tool for applying structural information to a given protein sequence. The resultant multiple alignment can be coloured according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol.

SPICE is a browser for protein sequences, structures and their annotations. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information. DALI Server. The Dali server is a network service for comparing protein structures in 3D.

PDBeMotif is an extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank PDB by combining protein sequence, chemical structure and 3D data in a single search. Currently it is the only tool that offers this kind of integration at this speed. PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins such as Kinases and the conserved structural features of their immediate environments either within the same specie or across different species.

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods see below to try to provide clues as the the protein's likely or possible function.

Often, where one method fails to provide any functional insight another may be more helpful. PBE server. ConSurf Server. The ConSurf server is a useful and user-friendly tool that enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional 3D structure, based on the phylogenetic relations between its close sequence homologues.

StrucToolsn is a set of tools intended to provide a convenient web interface to simple, commonly used structural biology calculations with PDB files. STING Millennium is a web based suite of programs that starts with the visualization of a molecular structure and leads the user through a series of operations resulting in an extensive structural analysis of the molecule.

This program allows to analyse contacts between two chains or within one chain in a given PDB file. HORI - Higher Order Residue Interactions, is a web server to compute higher order interactions pairwise interaction, triplet interactions and quadruple interactions in a protein structure.

MolTalk is a computational environment for doing Structural Bioinformatics. At the base of i. FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. Web resource for the identification of sequence-structure links. This resource brings together current state-of-the-art algorithmic methods for partitioning proteins into domains.

CDD Server. Dompred is a server designed to predict putative protein domains and their boundaries for a given protein sequence. The server uses several methods, from identifying obvious similarities to Pfam-A domain sequences to predicting domains using DomSSEA in cases where sequence searching has yielded no results.

Protein Peeling 3-D. The approach 'Protein Peeling' aims at cutting the 3D protein structure into a limited set of 'Protein Units'. A more precise definition of protein unit is a compact sub-region of the 3D structure corresponding to one sequence fragment. DOMpro is a web server to predict protein domain boundaries using 1D-Recursive Neural Networks and statistical methods.

DIAL is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein. Domain 3D. Domain 3D is a method developed by Willie Taylor to identify globular domains in protein structure. DHcL Domain Hierarchy and closed Loops is a server for the analysis of basic structural units of a protein. The server calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and van derWaals locks.

DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. CAVER is a software tool for analysis and visualisation of channels tunnels in protein structures. Channels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.

The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB. It addresses a situation where only few members of the large homologous family are characterized by experiment and function of others are unknown, either in a general sense or in details e.

Molecular surface of proteins with the electrostatic potential is a representation of protein three dimensional structures, which often gives some clues to infer the function of proteins. Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities.

It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. HotPatch finds unusual patches on the surface of proteins, and computes just how unusual they are patch rareness , and how likely each patch is to be of functional importance functional confidence FC.

The statistical analysis is done by comparing your protein's surface against the surfaces of a large set of proteins whose functional sites are known. For a given protein sequence or structure query, IBIS reports physical interactions observed in experimentally-determined structures for this protein. Pocket-Finder is a pocket detection algorithm based on Ligsite written by Hendlich et al Pocket-Finder works by scanning a probe radius 1.

Crystal structures as well as protein models can be used as the target structures. LIGSITE is a web server for the automatic identification of pockets on protein surface using the Connolly surface and the degree of conservation! The MEDock Maximum-Entropy based Docking web server is aimed at providing an efficient utility for prediction of ligand binding site.

Q-SiteFinder is a new method of ligand binding site prediction. It works by binding hydrophobic CH3 probes to the protein, and finding clusters of probes with the most favourable binding energy.