An assessment is presented for all submissions to the comparative modeling challenge in the 1996 Critical Assessment of Structure Prediction (CASP2). Of the original 12 target structures, 9 were solved prior to the meeting: 8 by X-ray crystallography and 1 by NMR spectroscopy. These targets varied o
CASP3 comparative modeling evaluation
β Scribed by T. Alwyn Jones; Gerard J. Kleywegt
- Publisher
- John Wiley and Sons
- Year
- 1999
- Tongue
- English
- Weight
- 385 KB
- Volume
- 37
- Category
- Article
- ISSN
- 0887-3585
No coin nor oath required. For personal study only.
β¦ Synopsis
We report our evaluation of the CASP3 comparative modelling competition. Our analysis covers the accuracy of the over-all fold, the bridging of insertions and deletions, and the adding of side-chains. We describe our attempts at automating aspects of the evaluation. Proteins
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We present results of comparative modeling on 11 targets from the CASP3 experiment. Our methods comprise the following steps: first, PSI-BLAST is used to find homologues of the target sequence in the nonredundant GenBank protein sequence database; second, after several iterations of PSI-BLAST, the r
We evaluate homology-derived 3D models of dihydrofolate reductase (DFR 1 ), phosphotransferase enzyme IIA domain (PTE2A 3 ), and mouse/human UBC9 protein (UBC9 24 ) which were submitted to the second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP). The DFR 1
Comparative modeling targets 1, 3, 9, and 17 were predicted by alignment of multiple sequences and structures, when available, followed by minimization using the program AMMP. The minimization used improved potentials, and distance restraints for regions of common structure. New prediction procedure
During a blind protein structure prediction experiment (the third round of the Critical Assessment of Techniques for Protein Structure Prediction; URL http://PredictionCenter.llnl.gov/ casp3/), four target proteins, T0047, T0048, T0055, and T0070, were modeled by comparison. These proteins display 6
The docking section of CASP2 is reviewed. Seven small molecule ligandprotein targets and one protein-protein target were available for predictions. Many of the small molecule ligand complexes involved serine proteases. Overall results for the small molecule targets were good, with at least one predi