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I-TASSER / Iterative Threading ASSEmbly Refinement

Allows automated protein structure prediction and structure-based function annotation. I-TASSER constructs, starting from the amino acid sequence, 3D structural models by reassembling fragments excised from threading templates. I-TASSER servers provides a confidence score (C-score) to estimate the models’ global accuracy. The I-TASSER Suite pipeline was tested in community-wide structure and function prediction experiments, including CASP10 and CAMEO.

RW

Provides distance-dependent atomic potential for protein structure modeling and structure decoy recognition. RW was derived from 1,383 high-resolution protein data bank (PDB) structures using an ideal random-walk chain as the reference state. The RW potential has been extensively optimized and tested on a variety of protein structure decoy sets and demonstrates a significant power in protein structure recognition and a strong correlation with the RMSD of decoys to the native structures. RW is freely available for download.

MODELLER

A software tool used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

3DRobot

A program devoted for automated generation of diverse and well-packed protein structure decoys. Given a native structure as input, 3DRobot first identifies diverse structure scaffolds from a non-redundant PDB library. Restraint-free fragment reassembly simulations are then performed to construct diverse full-length models. The final decoys are further refined at atomic-level by a two-step iterative energy minimization procedure to improve the hydrogen-binding networks and steric overlaps of the structures. 3DRobot aims to provide high-quality protein structural decoy sets for designing and training protein folding force field and folding simulation methods.

CABS-flex

An efficient procedure for the simulation of structure flexibility of folded globular proteins. Three consecutive steps follow the CABS simulation procedure: (i) structural clustering, (ii) models reconstruction to an all-atom representation and (iii) models superimposition, analysis and visualization. All these tasks are performed in the CABS-flex pipeline by well-established and extensively tested methods (typical for multi-scale protein modeling procedures) or general purpose scientific software.