Protein structure prediction begins well but ends badly Export

@article{citeulike:6102068, abstract = {The accurate prediction of protein structure, both secondary and tertiary, is an ongoing problem. Over the years many approaches have been implemented and assessed. Most prediction algorithms start with the entire amino acid sequence and treat all residues in an identical fashion independent of sequence position. Here we analyse blind prediction data to investigate whether predictive capability varies along the chain. Free modeling results from recent Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments are evaluated; as is the most up-to-date data from EVA, a fully-automated blind test of secondary structure prediction servers. Results demonstrate that structure prediction accuracy is dependent on sequence position. Both secondary structure and tertiary structure prediction are more accurate in regions near the amino(N)-terminus compared to analogous regions near the carboxy(C)-terminus. Eight out of the ten secondary structure prediction algorithms assessed by EVA perform significantly better in regions at the N-terminus. CASP data shows a similar bias, with N-terminal fragments being pre- dicted more accurately than fragments from the C-terminus. Two analogous fragments are taken from each model, the N-terminal fragment begins at the start of the most N-terminal secondary structure element (SSE) while the C-terminal fragment finishes at the end of the most C-terminal SSE. Each fragment is individually locally superimposed on to its respective native fragment. The relative terminal prediction accuracy (RMSD) is calculated on an intra-model basis. At a fragment length of 20 residues the N-terminal fragment is predicted with greater accuracy in 79\% of cases. Proteins 2009. {\copyright} 2009 Wiley-Liss, Inc.}, address = {University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, England, OX1 3TG}, author = {Saunders, Rhodri and Deane, Charlotte M.}, citeulike-article-id = {6102068}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.22646}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122670301/ABSTRACT}, doi = {10.1002/prot.22646}, issn = {1097-0134}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {bias, casp, prediction, protein, secondary, structure, tertiary}, number = {999A}, pages = {NA+}, posted-at = {2009-11-12 14:21:03}, priority = {2}, title = {Protein structure prediction begins well but ends badly}, url = {http://dx.doi.org/10.1002/prot.22646}, volume = {9999}, year = {2009} }

TY - JOUR ID - citeulike:6102068 L3 - citeulike-article-id:6102068 N2 - The accurate prediction of protein structure, both secondary and tertiary, is an ongoing problem. Over the years many approaches have been implemented and assessed. Most prediction algorithms start with the entire amino acid sequence and treat all residues in an identical fashion independent of sequence position. Here we analyse blind prediction data to investigate whether predictive capability varies along the chain. Free modeling results from recent Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments are evaluated; as is the most up-to-date data from EVA, a fully-automated blind test of secondary structure prediction servers. Results demonstrate that structure prediction accuracy is dependent on sequence position. Both secondary structure and tertiary structure prediction are more accurate in regions near the amino(N)-terminus compared to analogous regions near the carboxy(C)-terminus. Eight out of the ten secondary structure prediction algorithms assessed by EVA perform significantly better in regions at the N-terminus. CASP data shows a similar bias, with N-terminal fragments being pre- dicted more accurately than fragments from the C-terminus. Two analogous fragments are taken from each model, the N-terminal fragment begins at the start of the most N-terminal secondary structure element (SSE) while the C-terminal fragment finishes at the end of the most C-terminal SSE. Each fragment is individually locally superimposed on to its respective native fragment. The relative terminal prediction accuracy (RMSD) is calculated on an intra-model basis. At a fragment length of 20 residues the N-terminal fragment is predicted with greater accuracy in 79% of cases. Proteins 2009. © 2009 Wiley-Liss, Inc. IS - 999A JF - Proteins: Structure, Function, and Bioinformatics SN - 1097-0134 AD - University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, England, OX1 3TG TI - Protein structure prediction begins well but ends badly VL - 9999 SP - NA KW - bias KW - casp KW - prediction KW - protein KW - secondary KW - structure KW - tertiary AU - Saunders, Rhodri AU - Deane, Charlotte PY - 2009/// UR - http://dx.doi.org/10.1002/prot.22646 ER -