Loop Prediction

Name Sequence Structure % Content Experimental RXMD  

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HWT van Vlijmen, M Karplus. PDB-based protein loop prediction Parameters for selection and methods for optimization. I Mol Biol 267 975-1001, 1997. 

Fig. 8. Mutagenesis of the predicted ATP binding site. ATP is shown in proximity to amino acids in four loops predicted to form the ATP binding site in the nucleotide binding domain [49,134] and a fifth loop representing the phosphorylation site at Asp351 [97], Mutations and the corresponding Ca transport activity of the mutants relative to wild-type are indicated. From Clarke et al. [103).

Loop Prediction with Torsion Angle Sampling... 

The loop prediction algorithm implemented in the Protein Local Optimization Program (PLOP) is described in detail in [123]. During loop build-up,... 

We have tested the loop prediction algorithms on two sets of protein loops of known structure (see [101]). The first set is composed of the 57 nine-residue loops that were originally compiled by Fiser et al. [126] and by Xiang et al. [127]. The 35 13-residue loop set is the same as the one investigated by Zhu et al. [124],... 

In protein secondary structure prediction, where a three-category (a, P, and coil or loop) prediction is made, the accuracy can be measured by a 3 x 3 accuracy table, as in Rost and Sander (1993). 

Borrow core backbone from template structure, minus coil regions with insertions or deletions in the sequence alignment rebuild core side chains rebuild coil regions with loop prediction method in conjunction with side-chain prediction method. Core backbone and side chains may or may not be held fixed during loop prediction (e.g., CONGEN [95]). 

Methods for loop prediction are listed. When publicly available programs can be identified, they have been listed by name. Some methods have been implemented in publicly available programs, but no specific software or scripts are available. 

Abbreviations used in table MC - Monte Carlo aa - amino acid vdW - van der Waals potential Ig - immunoglobulin or antibody CDR - complementarity-determining regions in antibodies RMS -root-mean-square deviation r-dependent dielectric - distance-dependent dielectric constant e - dielectric constant MD - molecular dynamics simulation self-loops - prediction of loops performed by removing loops from template structure and predicting their conformation with template sequence bbdep - backbone-dependent rotamer library SCMF - self-consistent mean field PDB - Protein Data Bank Jones-Thirup distances - interatomic distances of 3 Ca atoms on either side of loop to be modeled. 

U. Lessel, D. Schomburg. Importance of anchor group positioning in protein loop prediction. Proteins. 1999, 37, 56-64. 

An optimum model-based predictive controller was developed to allow for control of molecular weight averages (intrinsic viscosities) and reactor temperatures in solid-state PET polymerizations, through manipulation of the inert gas temperatures and flowrates [ 199]. Simulation studies also showed that predictive controllers might lead to significant improvement of process operation in PVC suspension reactors, when temperatures are allowed to vary along the batch time [200]. Simulation studies performed for continuous styrene solution polymerizations showed that the closed-loop predictive control can also be used to stabilize the reactor operation at unstable open-loop steady-state conditions [201]. 

Rummey C, Metz G (2007) Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site. Proteins 66 160-171... 

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