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Inverse protein folding (IPF) software tools | Protein structure data analysis

Protein design aims to identify new protein sequences of desirable structure and biological function. Most current de novo protein design methods rely on physics-based force fields to search for low free-energy states following Anfinsen's…
OSPREY
Desktop

OSPREY Open Source Protein REdesign for You

Improves realistic in silico modeling of proteins. OSPREY is a suite of protein…

Improves realistic in silico modeling of proteins. OSPREY is a suite of protein redesign algorithms that are based on three characteristics: (1) a globally optimal protein design search allowing…

ProMuteHT
Desktop

ProMuteHT Protein Mutator High Throughput

Allows users to generate single and multiple in silico mutations. ProMuteHT is…

Allows users to generate single and multiple in silico mutations. ProMuteHT is a standalone program which intends to improve the way how mutants are designated thanks to a simplified command-line…

NewProt
Web

NewProt

Analyzes undesired side effects of predicted mutations. NewProt is a protein…

Analyzes undesired side effects of predicted mutations. NewProt is a protein engineering portal and a free one-stop-shop for protein structure related computational facilities. It relieves the…

ISAMBARD
Desktop

ISAMBARD Intelligent System for Analysis Model Building And Rational Design

Allows model building, rational design of biomolecules, and structural…

Allows model building, rational design of biomolecules, and structural analysis. ISAMBARD provides a generalized approach to in silico parametric design and optimization of de novo biomolecular…

FireProt
Web

FireProt

Automates design of multiple-point thermostable mutant proteins which combines…

Automates design of multiple-point thermostable mutant proteins which combines structural and evolutionary information in its calculation core. FireProt uses sixteen tools and three protein…

GAPSSIF
Desktop

GAPSSIF Genetic Algorithm for Protein Secondary Structure Inverse Folding

Solves protein secondary structure inverse folding problem. GAPSSIF employs…

Solves protein secondary structure inverse folding problem. GAPSSIF employs fragments of secondary sub-structures which explicitly participate in building up amino acid sequences. GAPSSIF takes four…

NIAS-Server
Web

NIAS-Server Neighbors Influence of Amino Acids and Secondary Structures

A server to help the analysis of the conformational preferences of amino acid…

A server to help the analysis of the conformational preferences of amino acid residues in proteins. NIAS is a web-based tool used to extract information about conformational preferences of amino acid…

RosettaBackrub
Web

RosettaBackrub

Implements the Backrub method, derived from observations of alternative…

Implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is…

EvoDesign
Web

EvoDesign

A web server to design optimal protein sequences of given scaffolds along with…

A web server to design optimal protein sequences of given scaffolds along with multiple sequence and structure-based features to assess the foldability and goodness of the designs. EvoDesign uses an…

RosettaDesign
Web

RosettaDesign

Identifies low energy amino acid sequences for target protein structures. The…

Identifies low energy amino acid sequences for target protein structures. The client provides the backbone coordinates of the target structure and specifies which residues to design. The server…

iRDP
Web

iRDP in-silico Rational Design of Proteins

A method for designing protein molecules with desired structure and biological…

A method for designing protein molecules with desired structure and biological function. iRDP web server is a one-stop tool for protein design which implements an in-silico “Analyze and Build”…

IPRO
Desktop

IPRO Iterative Protein Redesign & Optimization

Redesigns proteins to increase or give specificity to native or novel…

Redesigns proteins to increase or give specificity to native or novel substrates and cofactors. IPRO repeatedly randomly perturbs the backbones of the proteins around specified design positions,…

OptZyme
Desktop

OptZyme

Aims to design improved enzymatic activity (i.e., kcat or kcat/KM) with a novel…

Aims to design improved enzymatic activity (i.e., kcat or kcat/KM) with a novel substrate. The OptZyme key concept is to use transition state analogue compounds, which are known for many reactions,…

ScaffoldSelecti…
Desktop

ScaffoldSelection

Identifies potential attachment sites for smaller enzymatic motifs in a large…

Identifies potential attachment sites for smaller enzymatic motifs in a large set of protein structures. ScaffoldSelection was conceived to be a fast and initial search tool for potential sites. The…

Protein WISDOM
Web

Protein WISDOM

Assists in working on diseases such as HIV, cancer, complement diseases, and…

Assists in working on diseases such as HIV, cancer, complement diseases, and other autoimmune disorders. Protein WISDOM is an online tool that consists of two stages: (1) first it produces a…

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