Tertiary protein structure detection software tools
Protein tertiary structure refers to the 3-dimentional form of the protein, presented as a polypeptide chain backbone with one or more protein secondary structures, the protein domains. Determining the tertiary structure of a protein can be achieved by x-ray crystallography, nuclear magnetic resonance, and dual polarization interferometry. Alternatively, protein tertiary structure can be predicted using specific algorithm and software tools based on amino acid sequence.
A collection of programs, associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. CCP4 is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. A method for experimental X-ray data analysis called AUSPEX was integrated in CCP4.
Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer library, a simple energy function based on the library rotamer frequencies and a purely repulsive steric energy term, and a graph decomposition to solve the combinatorial packing problem. It calculates all the required energies and performs combinatorial optimization after which for each residue one of its rotamers will be marked as optimal.
Predicts 3D structure of a protein sequence. Phyre is a web application that investigates known homologues, builds a hidden Markov model (HMM) of the targeted sequence based on the detected homologues and scans it against a database of HMMs of known protein structures. It also provides advanced features such as a batch submission of a large number of protein sequences for modelling or Phyre Investigator, that allows users to analyze model quality, function and effects of mutations.
Provides a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. CNS allows heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. CNS is the result of an international collaborative effort among several research groups.
Provides automated structure prediction and analysis tools to infer protein structural information from genomic data. Robetta uses a fully automated implementation of the Rosetta software package for protein structure prediction. The software parses input sequences into domains and builds models for domains with sequence homology to proteins of known structure using comparative modeling, and models for domains lacking such homology.
Aggregates a number of protein annotation tools and provides services or software to allow users to perform truly scalable biological analyses. PSIPRED offers to the user the possibility to choose the method wanted to conduct the analysis. It proposes the following sequence and structure annotation methods: PSIPRED, GenTHREADER, pGenTHREADER, pDomTHREADER, MEMSAT-SVM/MEMSAT3, MEMPACK, BioSerf, MetSite, HSPred, DISOPRED2, DomPred and FFPred. The tool permits to select any number of appropriate simultaneous analyses across all the applicable methods and easily explore results.