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.
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.
Offers methods for structure prediction, design, and remodeling of proteins and nucleic acids. Rosetta provides a software suite for modeling macromolecular structures. This resource permits users to: (i) understand macromolecular interactions, (ii) design custom molecules, (iii) develop ways to search conformation and sequence space, and (iv) find energy functions for various biomolecular representations.
A web app to identifye automatically hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. HotSpot Wizard integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. The method provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries.favourite protein and for the design of mutations in site-directed mutagenesis and focused directed evolution experiments.
Helps deciding how to choose promising constructs for protein expression and crystallisation. ProteinCCD functions as a meta-server that collects information from prediction servers concerning secondary structure, disorder, coiled coils, transmembrane segments, domains and domain linkers. The server displays a condensed view of all results against the protein sequence. The user can study the output and choose interactively possible starts and ends for suitable protein constructs.
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.
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.
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.
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.
Consists of a modeling solution for biologics. BioLuminate is a suit that aims to address issues associated with the molecular design of biologics. The software enables protein-protein docking, protein engineering and antibody modeling. Users can also perform advanced computational analyses, including for instance helical stability/melting analysis from molecular dynamics (MD) simulations, or free energy perturbation (FEP) calculations of binding affinity and protein stability. The suite includes AggScore, which identifies aggregation hotspots.
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 structure. This software supplies an easy-to-use tool for the parametric design of such structures. It enables users to engage in the design process.
Designs proteins in a computational manner. iCFN can be employed for several purpose: side chain packing, protein design for single protein, binding affinity toward multiple targets, and multistate protein design with single or multiple substates. It offers variate functionalities to specify: maximum number of conformation, maximum single nucleotide polymorphism (SNP) threshold sequence, or maximum number of discrepancy sequence.
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 syntax as well as reducing energy needed for compute them. The pipeline can perform two types of calculation: large-to-small (LTS) amino acid substitutions and small-to-large (STL) amino acid mutations.
Allows users to automate batch sequence processing via a menu-driven graphical user interface. XLibraryDisplay is a program that performs through the interface of Microsoft Excel. It enables analysis of libraries of DNA and protein sequences for discovery projects. It permits data sets up to roughly over 10 000 sequences to be analyzed on a single personal computer.
Permits to fold protein atoms. SN-NeRF is a self-normalized method that can calculate Cartesian coordinates from torsion space parameters. It generates its three orthonormal vectors prior to self-normalizing.
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.
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.
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.
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 protein engineer from many simple household computational chores by providing integrated access a large number of computational facilities, to visualization and to artificial intelligent mutation validation.
Performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. Buccaneer is an application based on an automated technique for plotting protein chains in experimental electron density maps. It incorporates, in particular, the use of an oriented electron density probability target function to identify probable Cα positions. This method can also be used for low resolutions.
Provides an algorithm for protein design. BBK* is an ensemble-based algorithm search in order of binding affinity. It runs in time sublinear in the number of sequences. It not only computes the optimal sequences, but it also does combinatorially pruning the search space. This method enables computational protein design (CPD) by providing new Ka algorithms, with provable guarantees, for large-scale protein designs.