Which algorithm is used for protein structure prediction?

TASSER_WT: A Protein Structure Prediction Algorithm with Accurate Predicted Contact Restraints for Difficult Protein Targets.

What is I-TASSER used for?

I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences. It detects structure templates from the Protein Data Bank by a technique called fold recognition (or threading).

How accurate is tasser?

Combining C-score and protein length, the accuracy of the I-TASSER models can be predicted with an average error of 0.08 for TM-score and 2 Å for RMSD.

How protein structure is predicted?

There is a basic observation that similar sequences from the same evolutionary family often adopt similar protein structures, which forms the foundation of homology modeling. So far it is the most accurate way to predict protein structure by taking its homologous structure in PDB as template.

Which is the most accurate method for prediction of protein tertiary structure and why?

Presently, homology modeling is the most powerful method for predicting the tertiary structure of proteins in cases where a query protein has sequence similarity to a protein with known atomic structure.

How can we predict the secondary structure of protein?

Secondary structure of the proteins can be used to predict the tertiary structure since predicting only with amino acid sequence may not be sufficient. The secondary structure of proteins is determined by the pattern of hydrogen bonding.

What is tasser server?

The I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER) is an online resource for automated protein structure prediction and structure-based function annotation. In I-TASSER, structural templates are first recognized from the PDB using multiple threading alignment approaches.

How do you reference I-TASSER?

You are requested to cite following articles when you use the I-TASSER server: J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015).

How protein structure prediction methods are useful for research?

At the preSG stage, computationally predicted protein structures, built on structural templates from a variety of threading or homology-based algorithms, have proven to be helpful for drug screening and drug design, designing mutagenesis experiments, detecting active sites, solving the phase problem by molecular …

How can you predict the tertiary structure of a protein?

Homology modeling. Presently, homology modeling is the most powerful method for predicting the tertiary structure of proteins in cases where a query protein has sequence similarity to a protein with known atomic structure.

Is a protein secondary structure prediction tool?

Protein secondary structure refers to the local conformation proteins’ polypeptide backbone. Most commonly, the secondary structure prediction problem is formulated as follows: given a protein sequence with amino acids, predict whether each amino acid is in the α-helix (H), β-strand (E), or coil region (C).

Which secondary structure of protein is more stable?

It has been shown that α-helices are more stable, robust to mutations and designable than β-strands in natural proteins, thus designing functional all-α proteins is likely to be easier that designing proteins with both helices and strands; this has been recently confirmed experimentally.

What is the I-TASSER server?

The I-TASSER server is an integrated platform for automated protein structure and function prediction based on the sequence-to-structure-to-function paradigm. Starting from an amino acid sequence, I-TASSER first generates three-dimensional atomic models from multiple threading alignments and iterative structural assembly simulations.

How are protein function insights derived from 3D models?

Function insights of the target are then derived by re-threading the 3D models through protein function database BioLiP . I-TASSER (as ‘Zhang-Server’) was ranked as the No 1 server for protein structure prediction in recent community-wide CASP7 , CASP8, CASP9 , CASP10 , CASP11 , CASP12 , CASP13 , and CASP14 experiments.

What is the protein structure server?

The server is in active development with the goal to provide the most accurate protein structure and function predictions using state-of-the-art algorithms. The server is only for non-commercial use.