Structure prediction, from

Method for Protein Modeling and Design Applications to Docking and Structure Prediction from the Distorted Native Conformation. 

Fig. 23. Proposed active site arrangement of sn-glycerol-3-phosphate dehydrogenase (below), based on secondary structure predicted from the known primary structure, and on comparison with the known tertiary structure of glyceraldehyde-3-phosphate dehydrogenase (above). From the work of Rossmann and colleagues (94).

Challis GL, Ravel J (2000) Coelichelin, a New Peptide Siderophore Encoded by the Streptomyces coelicolor genome Structure Prediction from the Sequence of its Non-Ribosomal Peptide Synthetase. FEMS Microbiol Lett 187 111... 

Currently, methods of structure prediction from sequence perform poorly. The results of the biannual CASP experiment (Critical Assessment of techniques for protein Structure Prediction see http //predictioncenter.llnl. gov/) are equivocal to say the least. A recent report on the improvements of aligning target sequences to a structural template (67) indicates that over the last four CASP competitions there was no significant improvement in quality in this key step in the prediction process. Alignment remains the major source of error in all models based on less than 30% se-... 

Earlier structure predictions with coronins resulted in models of five-bladed P propellers, because only five WD repeats were recognised. However, many p propeller structures contain WD repeats with litde or no obvious sequence homology to the canonical sequence. Additionally, while typical WD repeats possess four to eight copies and up to 16 copies have been reported, almost all structures ofWD repeat proteins in the PDB contain seven blades per propeller. Keeping this in mind, more detailed analyses of coronins have been carried out and additional WD-like repeats were identified based on secondary structure prediction from amino acid sequences, indicating the presence of seven copies for coronins I(IA) - and 3 (IC) and 14 for coronin 7. The fold of a seven-bladed propeller was then confirmed by the crystal structure of a coronin 1 (lA) fragment. ... 

Atragyan, R. Totrov, M. Kuznetsov, D. ICM—a new method for protein modeling and design applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 2004, 15 (5), 488-506. 

To further characterize the tentative structures predicted from MALDI-MS data, components observed in the wild-type and knockout mouse spleen were subjected to MS/MS analyses using MALDI-TOF/TOF instrumentation. These experiments provide information on features like branching patterns, non-reducing end terminal structures, and sometimes linkage positions. O Figure 4 illustrates the MALDI-TOF/TOF spectrum of the molecular ion at m/z 2489. Major assignments are annotated and fragmentation patterns are shown schematically. 

In the absence of a high-resolution three-dimensional structure of a BFR, a tentative subunit conformation (Fig. 10) has been derived by secondary structure prediction from amino acid sequence data. A combined prediction based on eight different programs gave a helical dis-... 

FIGURE 6 Frequency of each substituent at RI, R2, R3, and R4 in structures active against CXCR2 (upper panel) and BK-I (lower panel). Active structures predicted from the encoded library, against either CXCR2 or BK-I receptors, are evaluated in terms of substituents at each point of variation. The frequency with which each substituent is found in the active structures is indicated in comparison to all other possibilities at that position RI = 31 R2 = 31 R3 = 4 R4 = 38. 

The modeling approach is generally useful if the query structure is not contained in the database. Although the methods for structure prediction from infrared spectra introduced here can give quite accurate proposals, several considerations have to be taken into account. 

Frishman, D. and Argos, R, Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence, Prot. Eng., 9, 133, 1996. 

Brendel, V., L. Xing, and W. Zhu. 2004. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20 1157-69. 

Figure 5.48. The COSY crosspeak for an A3X group illustrating the structure predicted from Pascal s triangle.

STRUCTURE PREDICTION FROM SEQUENCE BY STATISTICAL METHODS... 

There is a considerable impetus to predict accurately protein structures from sequence information because of the protein sequence/structure deficit as a consequence of the genome and full-length cDNA sequencing projects. The molecular mechanical (MM) approach to modeling of protein structures has been discussed in section 9.2, and the protein secondary structure prediction from sequence by statistical methods has been treated in section 9.5. The prediction of protein structure using bioinformatic resources will be described in this subsection. The approaches to protein structure predictions from amino acid sequences (Tsigelny, 2002 Webster, 2000) include ... 

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