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The Swiss-model Workspace integrates programs and databases required for protein structure prediction and modelling in a web-based workspace. Depending on the complexity of the modelling task, different modes of use can be applied, in which the user has different levels of control over individual modelling steps: automated mode, alignment mode, and project mode.
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...
A dynamic programming algorithm for the prediction of a restricted class (H-type) of RNA pseudoknots. Yes: sourcecode, webserver [20] RNA123: Secondary structure prediction via thermodynamic-based folding algorithms and novel structure-based sequence alignment specific for RNA. Yes: webserver: RNAfold: MFE RNA structure prediction algorithm.
A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues Automated webserver and some downloadable programs RaptorX: remote homology detection, protein 3D modeling, binding site prediction
I-TASSER is a template-based method for protein structure and function prediction. [1] The pipeline consists of six consecutive steps: 1, Secondary structure prediction by PSSpred; 2, Template detection by LOMETS [6] 3, Fragment structure assembly using replica-exchange Monte Carlo simulation [7]
RaptorX is the successor to the RAPTOR protein structure prediction system. RAPTOR was designed and developed by Dr. Jinbo Xu and Dr. Ming Li at the University of Waterloo. RaptorX was designed and developed by a research group led by Prof. Jinbo Xu at the Toyota Technological Institute branch at Chicago.
The protein structure prediction remains an extremely difficult and unresolved undertaking. The two main problems are the calculation of protein free energy and finding the global minimum of this energy. A protein structure prediction method must explore the space of possible protein structures which is astronomically large.
Thus, structure prediction software which relies on such homology can be expected to perform poorly in predicting structures of de novo proteins. [18] To improve accuracy of structure prediction for de novo proteins, new softwares have been developed. Namely, ESMFold is a newly developed large language model (LLM) for the prediction of protein ...