Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Protein-metal site detection software tools | Structure data analysis

It has been estimated that 30–40% of proteins require one or more metal ions to be able to carry out their biological function in cells (Andreini et al., 2009; Andreini et al., 2008). This proportion depends on the specific organism or tissue…
MetalPredator
Web

MetalPredator

Predicts iron-sulfur proteins from protein sequence(s). MetalPredator…

Predicts iron-sulfur proteins from protein sequence(s). MetalPredator integrates an existing domain-based approach (Andreini et al., 2011) with a new one designed to search for metal-binding motifs…

CaoEtAl2017
Web

CaoEtAl2017

Identifies metal ion binding sites. The web-server predicts metal binding sites…

Identifies metal ion binding sites. The web-server predicts metal binding sites without the use of 3D structures, using only sequence information.

CMM
Web

CMM CheckMyMetal

A sophisticated, user-friendly web-based method to evaluate metal-binding sites…

A sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set…

BioMe
Dataset

BioMe Biologically relevant Metals

A web-based platform for calculation of various statistical properties of…

A web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal…

MetalionRNA
Web

MetalionRNA

Predicts positions of metal ions (magnesium, sodium and potassium), based on…

Predicts positions of metal ions (magnesium, sodium and potassium), based on the analysis of binding sites in experimentally solved RNA structures. The MetalionRNA program is available as a web…

mFASD
Desktop

mFASD

Discriminates different types of metal-binding sites effectively based on 3D…

Discriminates different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction. mFASD captures the characteristics of a…

MetalDetector
Web
Desktop

MetalDetector

Identifies CYS and HIS involved in transition metal protein binding sites,…

Identifies CYS and HIS involved in transition metal protein binding sites, starting from sequence alone. A major new feature of release 2.0 is the ability to predict which residues are jointly…

MetSite
Web

MetSite

Represents a fully automatic approach for the detection of metal-binding…

Represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in…

MINAS
Dataset

MINAS Metal Ions in Nucleic AcidS

Compiles the detailed information on innersphere, outersphere and larger…

Compiles the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today…

MetalPDB
Dataset

MetalPDB

Collects and allows easy access to the knowledge on metal sites in biological…

Collects and allows easy access to the knowledge on metal sites in biological macromolecules, starting from the structural information contained in the Protein Data Bank (PDB). The web interface of…

GRE4Zn
Web

GRE4Zn Geometric REstiction for Zinc-binding

Identifies zinc-binding sites in protein structures. GRE4Zn restricts the…

Identifies zinc-binding sites in protein structures. GRE4Zn restricts the distances between zinc and its coordinating atoms. It has been used to perform a large-scale study on the structurally…

TEMSP
Desktop

TEMSP 3D TEmplate-based Metal Site Prediction

A structure-based method to predict zinc-binding sites. TEMSP significantly…

A structure-based method to predict zinc-binding sites. TEMSP significantly improves over previously reported best methods in predicting as many as possible true ligand residues for zinc with minimum…

FindGeo
Desktop
Web

FindGeo

Allows to quickly and easily determine the coordination geometry of selected,…

Allows to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure…

MetalS3
Web

MetalS3 Metal Sites Similarity Search

A database search tool to find structurally similar Minimal Functional Sites…

A database search tool to find structurally similar Minimal Functional Sites (MFSs) to a given MFS. For each MFS, the best superposition is kept. All these superpositions are then ranked according to…

CHED
Web

CHED

Predicts 3D intra-chain protein binding sites for transition metals (Zn, Fe,…

Predicts 3D intra-chain protein binding sites for transition metals (Zn, Fe, Mn, Cu, Ni, Co, and Ca and Mg sites that can be replaced by a transition metal). The algorithm searches for a triad of…

MetalS2
Desktop
Web

MetalS2

A software tool for the structural alignment of Minimal Functional Sites (MFSs)…

A software tool for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the…

FEATURE
Web

FEATURE

A Bayesian classifier using known zinc binding sites as positive training…

A Bayesian classifier using known zinc binding sites as positive training examples and nonmetal binding regions that nonetheless contain residues frequently observed in zinc sites as negative…

Mespeus
Dataset

Mespeus

Lists metal protein interactions whose geometry has been experimentally…

Lists metal protein interactions whose geometry has been experimentally determined and allows them to be visualized. This can contribute to the modeling process.

SeqCHED
Web

SeqCHED

Enables the user to analyze a translated gene sequence for soft (Zn, Fe, Ni,…

Enables the user to analyze a translated gene sequence for soft (Zn, Fe, Ni, Cu, Co, Mn), and promiscuous hard (Mg, Ca), metal-ion binding sites. The application checks for homology of your target…

COMe
Dataset

COMe Co-Ordination of Metals

Represents the ontology for bioinorganic and other small molecule centres in…

Represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM), 'molecule'…

MIPS
Dataset

MIPS Metal Interactions in Protein Structures

A database of metals in the three-dimensional macromolecular structures…

A database of metals in the three-dimensional macromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed…

MetLigDB
Dataset

MetLigDB

A publicly accessible web-based database on which the interactions between a…

A publicly accessible web-based database on which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in…

MeRNA
Dataset

MeRNA

Contains information relating to binding of 9764 metal ions corresponding to 23…

Contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements, in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using…

MDB
Dataset

MDB Metalloprotein Database and Browser

A web-accessible resource for metalloprotein research. MDB offers the…

A web-accessible resource for metalloprotein research. MDB offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available…

MIB
Web

MIB Metal Ion-Binding

Predicts metal ion-binding residues and generates the predicted metal ion-bound…

Predicts metal ion-binding residues and generates the predicted metal ion-bound 3D structure. MIB is a web server that provides the metal ions docking after prediction. Twelve kinds of metal ions…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.