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Protein design 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 thermodynamic hypothesis.

Source text:
(Mitra et al., 2013) EvoDesign: De novo protein design based on structural and evolutionary profiles. Nucleic Acids Res.

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OSPREY / Open Source Protein REdesign for You
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Performs in silico modeling of proteins. OSPREY compiles several protein redesign algorithms based on three characteristics: (1) a protein design search allowing computational predictions; (2) features for modeling proteins and ligands as ensembles of low-energy structures; and (3) a way to determine conformational changes induced by mutations to the protein sequence. It can be used for enzyme or antibody design as well as for experimental studies.
FireProt
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 engineering strategies for making reliable protein designs. It allows user to analyze and modify the design of thermostable mutants. The graphical user interface (GUI) provides user to interactively analyze individual mutations selected as a part of energy, or evolution-based approach together with the ability to design their own multiple-point.
RosettaDesign
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 returns to the client the sequences, coordinates and energies of the designed proteins. The simulations are performed using the design module of the Rosetta program (RosettaDesign). RosettaDesign uses Monte Carlo optimization with simulated annealing to search for amino acids that pack well on the target structure and satisfy hydrogen bonding potential.
EvoDesign
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 evolution-profile-based Monte Carlo search with the profiles constructed from homologous structure families in the Protein Data Bank. A set of local structure features, including secondary structure, torsion angle and solvation, are predicted by single-sequence neural-network training and used to smooth the sequence motif and accommodate the physicochemical packing.
IPRO / Iterative Protein Redesign & Optimization
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, identifying the lowest energy combination of rotamers, and determining if the new design has a lower binding energy than previous ones. The iterative nature of this process allows IPRO to make additive mutations to the protein sequence that collectively improve the specificity towards the desired substrates and/or cofactors.
OptZyme
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, as proxies for the typically unknown transition state structures. Mutations that minimize the interaction energy of the enzyme with its transition state analogue, rather than with its substrate, are identified that lower the transition state formation energy barrier. Furthermore, restraints can be imposed to retain catalytic functionality.
ScaffoldSelection
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 results offered by ScaffoldSelection should then be refined by adequate filtering or minimization steps, for example by a more thorough investigation of the substrate or transition-state geometry in a match attachment site, and a recapitulation of the attachment geometry with a more fine-grained rotamer library. ScaffoldSelection can help to reduce the search space for such a more extensive analysis considerably.
GAPSSIF / Genetic Algorithm for Protein Secondary Structure Inverse Folding
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 steps to design it: (i) loading fragment repository; (ii) making knowledge-based population using fragment repository; (iii) enriching knowledge-based population; (iv) searching through sequence space. GAPSSIF algorithm performs successful design for its input secondary structure scaffold.
NIAS-Server / Neighbors Influence of Amino Acids and Secondary Structures
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 residues and secondary structures in experimental-determined protein templates. This information is useful, for example, to characterize folds and local motifs in proteins, molecular folding, and can help the solution of complex problems such as protein structure prediction, protein design, among others.
RosettaBackrub
Obsolete
Implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein-protein interfaces. The three protocols have been validated on experimental data.
iRDP / in-silico Rational Design of Proteins
Obsolete
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” approach to the rational protein design problem. The tool is divided into four modules, namely iCAPS, iMotifs, iMutants and iStability. iCAPS compares large number of protein structures for factors contributing to their structural stability. iStability implements known thermostabilization strategies in proteins for identification of potential stabilizing mutation sites. iMutants evaluates any mutations based on change in local interaction framework and degree of residue conservation at the mutation sites.
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