The protein structure prediction problem could be solved using the current PDB library.

@article{citeulike:126997, abstract = {For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35\% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 A with approximately 82\% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 A (97\% of them below 4 A). On average, the RMSD of full-length models is 2.25 A, with aligned regions improved from 2.5 A to 1.88 A, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments.}, address = {Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA.}, author = {Zhang, Y. and Skolnick, J. }, citeulike-article-id = {126997}, doi = {10.1073/pnas.0407152101}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {casp, homology, modelling, pdb, prediction, protein, structure}, month = {January}, number = {4}, pages = {1029--1034}, posted-at = {2008-06-12 07:42:10}, priority = {2}, title = {The protein structure prediction problem could be solved using the current PDB library.}, url = {http://dx.doi.org/10.1073/pnas.0407152101}, volume = {102}, year = {2005} }

TY - JOUR ID - citeulike:126997 L3 - citeulike-article-id:126997 TI - The protein structure prediction problem could be solved using the current PDB library. JF - Proc Natl Acad Sci U S A VL - 102 IS - 4 SP - 1029 EP - 1034 AD - Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA. SN - 0027-8424 N2 - For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 A with approximately 82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 A (97% of them below 4 A). On average, the RMSD of full-length models is 2.25 A, with aligned regions improved from 2.5 A to 1.88 A, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. KW - casp KW - homology KW - modelling KW - pdb KW - prediction KW - protein KW - structure AU - Zhang, Y AU - Skolnick, J PY - 2005/01/25/ UR - http://dx.doi.org/10.1073/pnas.0407152101 ER -