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.
Assists users with the simulation of structure flexibility of folded globular proteins. CABS-flex provides a simulation engine that allows users to reproduce large-scale conformational transitions of protein systems. It includes three consecutive steps: (i) structural clustering, (ii) model reconstruction to an all-atom representation and (iii) model superimposition, analysis and visualization. This method is available as a standalone program and as a web application.
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.
Finds decoy molecules for a given target. Decoyfinder is an application designed to build target-specific decoy sets. The software selects decoys both :(i) similar to active ligands according to five physical descriptors and; (ii) not chemically similar to any of the active ligands used as an input. Users can adjust the levels of similarity and difference. The algorithm for decoy selection implemented in the same software as the DUD database and other benchmarks.
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.
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.
Allows users to predict structural similarity between native structures and their decoys. SVR_CAF is a scoring function for protein structure selection that proposes a machine learning score. It sorts the structures by using energy considerations and network topology characters. The application incorporates three normalized scores: residue contact energy, the amino acid network and the fast Fourier transform.
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