Folding inverse

Godzik A, A Kolinski and JSkolnick 1993, DeNovo and Inverse Folding Predictions of ProteinStm and Dynamics. Journal of Computer-Aided Molecular Design 7 397-438. 

With the realization that there are only a limited number of stable folds and many unrelated sequences that have the same fold, biologically oriented computer scientists started to address what is called the inverse folding problem namely, which sequence patterns are compatible with a specific fold If this question can be answered, such patterns could be used to search through the genome sequence databases and extract those sequences that have a specific fold, such as the cx/p barrel or the immunoglobulin fold. 

Inverse folding can be viewed as an optimization problem that can be treated with simple heuristics. This is what the RNAinverse program does for you. Input for the RNAinverse program consists of an RNA secondary structure (the target) in bracket notation (on the first line), optionally followed by a sequence to be used as the starting point of the optimization (otherwise a random start sequence is used). 

Inverse Folding and Threading (350-353). This is the ultimate in motif recognition One makes use of the ever-increasing database of known three-dimensional structures to generate a set of 3D folding motifs for proteins. The sequence of an unknown structure... 

Tectonic breaching within the GEA is mostly related to Cretaceous to Tertiary compressional or tran-spressional deformation and is manifested by two processes. Firstly, extension occurs above the neutral surface of inversion folds (Fig. 8a), thereby creating a pattern of radial tension fractures, extending upwards from the seal into the overlying section. Radial fractures will not form below the neutral surface of the fold limb which is in compression. As a consequence, reservoir objectives lying above or close to the neu-... 

G. M. Crippen. Failures of inverse folding and threading with gapped alignment. Proteins. 1996, 26, 167-171. 

Other theoretical structure prediction methods, such as simulating folding pathways, lattice models, simulations and predictions, inverse folding (i.e. designing the best sequence for a fold/structure), physical methods (based on finding minimum energy conformations for realistic physicochemical potentials), are not discussed here. 

The rationale is that in this way it is possible to restrict the predictions to rigid elements of the core, for which the assumption of closeness in space as reflected in the covariance of their mutational behavior is, in principle, more valid. Then, inverse folding [226] is used to select compatible fragments in contact, thereby enriching the number and identity of predicted side-chain contacts. Parenthetically, we note that for topological elements that are known to touch, this procedure produces contacts of which 67% are correct within +1 residue. This is of comparable accuracy to the situation where the contacts are predicted. Of course, they do not employ any information about the native structure in the prediction protocol. The final outcome of the prediction protocol is a set of noisy secondary and tertiary restraints. 

A. Godzik, A. Kolinski, and J. Skolnick, Topology fingerprint approach to the inverse folding problem. J. Mol Biol 111, 221-23% (1992). 

The de novo protein design relies on understanding the relationship between the amino acid sequence of a protein and its three-dimensional struc-fMre.41 42.43,44,45,46 problem begins with a known protein three-dimensional structure and requires the determination of an amino acid sequence compatible with this structure. At the outset the problem was termed the inverse folding problem since protein design has intimate links to the well-known protein folding problem." ... 

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