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Structure validation software tools | Protein data analysis

Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues.Source text:(Sehnal et al., 2015) ValidatorDB: database of…
VERIFY3D
Web

VERIFY3D

Determines the compatibility of an atomic model (3D) with its own amino acid…

Determines the compatibility of an atomic model (3D) with its own amino acid sequence by assigning a structural class based on its location and environment and comparing the results to good…

WHAT_CHECK
Desktop

WHAT_CHECK

A suite of programs to assess the "stereochemical quality" of a given…

A suite of programs to assess the "stereochemical quality" of a given protein structure.

SIRAH tools
Desktop

SIRAH tools Southamerica Initiative for a Rapid and Accurate Hamiltonian tools

A toolkit for mapping, backmapping and visualization of coarse-grained (CG)…

A toolkit for mapping, backmapping and visualization of coarse-grained (CG) models. SIRAH tools provides a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes,…

ValidatorDB
Dataset

ValidatorDB

Offers a new step in this direction, in the form of a database of validation…

Offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy…

SARAMA
Desktop

SARAMA

A standalone suite of programs to plot the distribution of residues embedded at…

A standalone suite of programs to plot the distribution of residues embedded at a globular protein interior in the Complementarity Plots. The complementarity plot (CP) is based on packing and…

MotiveValidator
Web

MotiveValidator

A web-based application for the validation of ligands and residues in PDB or…

A web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward…

SUBWAI
Desktop

SUBWAI SUBoptimal Weighted alIgnment

Predicts protein structure by using a threading strategy with SuboPtimal…

Predicts protein structure by using a threading strategy with SuboPtimal Alignment Diversity (SPAD). SUBWAI generates classified target-template alignments and determines a SPAD value for each…

SUPRB
Desktop

SUPRB Suboptimal alignment-based PRoBabilistic residue

Provides a template-based structure prediction method using suboptimal…

Provides a template-based structure prediction method using suboptimal alignment information. SUPRB considers interaction pairs in a probabilistic fashion by counting residue interactions in…

Fitmunk
Web

Fitmunk

Provides a framework for fitting conformations on a fixed backbone into…

Provides a framework for fitting conformations on a fixed backbone into electron density. Current Fitmunk applications can assist in protein model building, refinement and validation. Fitmunk was…

PHENIX
Desktop

PHENIX Python-based Hierarchical ENvironment for Integrated Xtallography

Allows automated determination of molecular structures using X-ray…

Allows automated determination of molecular structures using X-ray crystallography and other methods. PHENIX is a software suite which provides a range of tools for the analysis, validation and…

PROCHECK
Desktop

PROCHECK

Checks the stereochemical quality of a protein structure, producing a number of…

Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the…

Coot
Desktop

Coot Crystallographic Object-Oriented Toolkit

A molecular-graphics application primarily aimed to assist in model building…

A molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Coot displays maps and models and allows model manipulations such as…

ProSA-web
Desktop
Web

ProSA-web Protein Structure Analysis-web

A tool for experimental structure determinations and modelling studies. ProSA…

A tool for experimental structure determinations and modelling studies. ProSA has a large user base and is employed in the refinement and validation of experimental protein structures and in…

RECOORD
Dataset

RECOORD

A database that contains recalculated structures for 500+ protein entries from…

A database that contains recalculated structures for 500+ protein entries from the Protein Data Bank (PDB). RECOORD can be used by the structural biology community for further development of…

Mumbo
Desktop

Mumbo

Simplifies the crystal structure-determination process. Mumbo helps to identify…

Simplifies the crystal structure-determination process. Mumbo helps to identify the correct orientation of the side chains during refinement. It can resolve the side-chain positioning problem in…

Mogul
Desktop

Mogul

A program for automated retrieval of molecular geometry data from the Cambridge…

A program for automated retrieval of molecular geometry data from the Cambridge Structural Database (CSD). The program uses a system of keys to encode the chemical environments of fragments (bonds,…

ValLigURL
Web

ValLigURL

It can be used by practising crystallographers to validate the geometry of a…

It can be used by practising crystallographers to validate the geometry of a ligand and to compare the conformation of a ligand with all instances of that ligand in the structural database (wwPDB).…

OOPS
Desktop

OOPS Open Protein Simulator

It is a program that offers a flexible framework where different approaches and…

It is a program that offers a flexible framework where different approaches and algorithms for protein folding, dynamics and structure prediction can be tested and benchmarked with ease. OOPS is…

MolProbity
Web

MolProbity

A structure-validation web service that provides broad-spectrum solidly based…

A structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids.

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