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Structure refinement software tools | Protein data analysis

Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states.Source text:(Bhattacharya and Cheng 2013) i3Drefine software for…
3Drefine
Web
Desktop

3Drefine

An interactive web server for consistent and computationally efficient protein…

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…

REFMAC5
Desktop

REFMAC5 Refinement of Macromolecular Structures

Aids crystallographic refinement at medium and higher resolutions over the past…

Aids crystallographic refinement at medium and higher resolutions over the past few decades. With REFMAC5, structural information may be utilized in various forms, such as secondary-structure…

GalaxyRefine
Web
Desktop

GalaxyRefine

A web server for protein model structure refinement that is particularly…

A web server for protein model structure refinement that is particularly successful in improving local structure quality as demonstrated by the tests on CASP refinement category targets and CASP10…

Princeton TIGRESS
Web
PREFMD
Web

PREFMD Protein structure REFinement via Molecular Dynamics

Offers a protein structure refinement web server. PREFMD implements an…

Offers a protein structure refinement web server. PREFMD implements an extensive molecular dynamics (MD)-based refinement protocol based on the best-performing refinement method. It relies on initial…

ReFOLD
Web

ReFOLD

Identifies and fixes likely errors in user supplied 3D models of proteins via…

Identifies and fixes likely errors in user supplied 3D models of proteins via successive rounds of refinement. ReFOLD allows users to quickly visualize the key residue locations, which are likely to…

SPRING
Desktop

SPRING Single Particle Reconstruction from Images of kNown Geometry

Provides a single-particle based helical reconstruction package for electron…

Provides a single-particle based helical reconstruction package for electron cryo-micrographs. SPRING has been used to determine 3D structures of a variety of highly ordered and less ordered…

GalaxyRefineCom…
Web

GalaxyRefineComplex

Adapts the effective sampling method of GalaxyRefine by performing repetitive…

Adapts the effective sampling method of GalaxyRefine by performing repetitive repacking of interface side chains followed by short MD relaxations. GalaxyRefineComplex is a method for refining…

MULTICOM
Web
Desktop

MULTICOM

Combines multiple sources of information and complementary methods at all five…

Combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model…

KoBaMIN
Web

KoBaMIN

Provides an online interface to a simple, consistent and computationally…

Provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server…

NOC
Desktop

NOC

Uses as an easy-to-use protein explorer for structure visualization, analysis.…

Uses as an easy-to-use protein explorer for structure visualization, analysis. NOC is a powerful software for crystallographic mapping, modelling and refinement and an efficient viewer for…

FG-MD
Web

FG-MD

A molecular dynamics (MD) based algorithm for atomic-level protein structure…

A molecular dynamics (MD) based algorithm for atomic-level protein structure refinement. Given an initial protein structure, FG-MD first identifies analogous fragments from the PDB by the structural…

ModRefiner
Desktop
Web

ModRefiner

An algorithm for atomic-level, high-resolution protein structure refinement,…

An algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are…

REMO
Web

REMO

An algorithm for constructing protein atomic structures from C-alpha traces by…

An algorithm for constructing protein atomic structures from C-alpha traces by optimizing the backbone hydrogen-bonding networks. The REMO algorithm has been exploited in the recent CASP8 experiment…

SCOPE
Desktop

SCOPE Semi Classical Open Source Protein Energy

Allows users to recreate structures and explore the calculated non-bonded…

Allows users to recreate structures and explore the calculated non-bonded energy. SCOPE is a program utilizing the topology information to calculate Van der Waals energy and electrostatic energy of…

PrimeX
Desktop

PrimeX

Allows protein crystal structure refinement. PrimeX is an X-ray crystal…

Allows protein crystal structure refinement. PrimeX is an X-ray crystal structure refinement program which provides several features such as maximum-likelihood reciprocal-space minimization,…

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