List Of Protein Structure Prediction Software

Selasa, 12 September 2017

List Of Protein Structure Prediction Software - Protein Domain Prediction

This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.

Software highlight

source : raptorx.uchicago.edu

Protein structure prediction is a broad problem that roughly consists of 1) structure prediction with information from similar proteins (Homology Modeling or Template Based Modeling) and structure prediction without any assistance from or knowledge of similar proteins (ab initio structure prediction or Free Modeling). Software for either of these can be fully automated or require human intervention.

Robetta from the Baker Laboratory at the University of Washington Robetta is the top-performing Homology Modeling server at CASP 2016 (Template Based Modeling) CASP12 and is the top performing server in the Continuous Automated Model EvaluatiOn testing server as of June 3, 2017, and has held that number one rank at least since 2014 (CAMEO) CAMEO. Robetta is a ten-step pipeline of multiple bioinformatics tools, notably the Rosetta software suite of algorithms for computational modeling and analysis of protein structures. Rosetta development began in the laboratory of Dr. Baker as a structure prediction tool but since then has been adapted to solve common computational macromolecular problems. Extensions of Rosetta include Foldit, which seeks to investigate the pattern-recognition and puzzle-solving abilities inherent to the human mind in order to create more successful computer protein structure prediction software.

I-TASSER is the best server for Free Modeling protein structure prediction according to the 2006â€"2016 CASP experiments (CASP7, CASP8, CASP9, CASP10, CASP11, and CASP12). The standalone I-TASSER package is freely available for download.

HHpred was the leading server for template-based protein structure prediction in the 2010 CASP9 experiment. It has a median response time of a few minutes instead of days like other top-performing servers. HHpred is often used for remote homology detection and homology-based function prediction. It runs with the free, open-source software package HH-suite for fast sequence searching, protein threading and remote homology detection.

DNASTAR's NovaFold is protein structure prediction software that is based on I-TASSER. NovaFold utilizes the I-TASSER algorithms that combine threading and ab initio folding technologies to build accurate, full 3D atomic models of proteins with previously unknown structures. NovaFold is available locally and as cloud-based software.

RaptorX excels at aligning hard targets according to the 2010 CASP9 experiments. RaptorX generates the significantly better alignments for the hardest 50 CASP9 template-based modeling targets than other servers including those using consensus and refinement methods. The RaptorX server is available at server

MODELLER is a popular software tool for producing homology models by satisfaction of spatial restraints using methodology derived from NMR spectroscopy data processing. The ModWeb comparative protein structure modeling web-server uses primarily MODELLER for automatic comparative modeling.

TIP is a knowledgebase of STRUCTFAST models and precomputed similarity relationships between sequences, structures, and binding sites. Several distributed computing projects concerning protein structure prediction have also been implemented, such as the Folding@home, Rosetta@home, Human Proteome Folding Project, Predictor@home, and TANPAKU.

BBSP (Building Blocks Structure Predictor) is a program that makes use of Hybrid template-based approaches, which associate fragment conformations for the sequence and detect distant fold similarities based on the fragment similarities . Also, such program is assisted by a secondary structure prediction algorithm named HCAM, which is mainly based on hydropathy profile analysis and is included in the BBSP tools suite.

MOE (Molecular Operating Environment) is a platform for protein and small molecule modelling and drug discovery applications, including homology modelling, with custom, knowledge-based routines for different protein and antibody families, e.g. GPCRs, kinases, etc. There are also applications for analysing modelled or experimental structures, and making them suitable to use in drug discovery programs.