Crystalp2: Sequence-based protein crystallization propensity prediction

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Kurgan, Lukasz ^a   Razib, Ali A ^a   Aghakhani, Sara ^a   Dick, Scott ^a   Mizianty, Marcin ^a   Jahandideh, Samad ^b  

^a UNIVERSITY OF ALBERTA   (Canada)

^b SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; ENTROPY; PREDICTION; PROTEIN DETERMINATION; SENSITIVITY AND SPECIFICITY; STRUCTURAL GENOMICS; ARTIFICIAL INTELLIGENCE; CHEMISTRY; CRYSTALLIZATION; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ANALYSIS;

ARTIFICIAL INTELLIGENCE; CRYSTALLIZATION; DATABASES, PROTEIN; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 69249163807     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-50     Document Type: Article

References (48)

1. The impact of structural genomics: expectations and outcomes. JM Chandonia SE Brenner, Science 2006 311 347 351 10.1126/science.1121018 16424331 (Pubitemid 43132652)
2. Protein models in drug discovery. M Norin M Sundström, Curr Opin Drug Discov Devel 2001 4 284 290 11560059
3. Recent structural and computational insights into conformational diseases. X Fernndez-Busquets NS de Groot D Fernandez S Ventura, Curr Med Chem 2008 15 1336 49 10.2174/092986708784534938 18537613 (Pubitemid 351997803)
4. Determining membrane protein structures: still a challenge! JJ Lacapère E Pebay-Peyroula JM Neumann C Etchebest, Trends Biochem Sci 2007 32 6 259 70 10.1016/j.tibs.2007.04.001 17481903 (Pubitemid 46881229)
5. Structure and mechanism of the M2 proton channel of influenza A virus. JR Schnell JJ Chou, Nature 2008 451 591 595 10.1038/nature06531 18235503 (Pubitemid 351186272)
6. Regulation of T cell receptor activation by dynamic membrane binding of the CD3epsilon cytoplasmic tyrosine-based motif. C Xu E Gagnon ME Call JR Schnell CD Schwieters CV Carman JJ Chou KW Wucherpfennig, Cell 2008 135 4 702 713 10.1016/j.cell.2008.09.044 19013279
7. Structural genomics, round 2. R Service, Science 2005 307 1554 1558 10.1126/science.307.5715.1554 15761136 (Pubitemid 40354718)
8. Target selection for structural genomics. SE Brenner, Nat Struct Biol 2000 7 967 969 10.1038/80747 11104002 (Pubitemid 30823279)
9. Implications of structural genomics target selection strategies: Pfam whole genome, and random approaches. JM Chandonia SE Brenner, Proteins 5000 58 166 179 10.1002/prot.20298
10. High-throughput protein crystallization. R Hui A Edwards, J Struct Biol 2003 142 154 61 10.1016/S1047-8477(03)00046-7 12718927 (Pubitemid 36457897)
11. Strategies for structural proteomics of prokaryotes: quantifying the advantages of studying orthologous proteins and of using both NMR and x-ray crystallography approaches. A Savchenko A Yee A Khachatryan T Skarina E Evdokimova M Pavlova A Semesi J Northey S Beasley N Lan R Das M Gerstein CH Arrowmith AM Edwards, Proteins 2003 50 392 399 10.1002/prot.10282 12557182 (Pubitemid 36158453)
12. Practical implementations for improving the throughput in a manual crystallization setup. C Biertumpfel J Basquin D Suck, J Appl Cryst 2005 38 568 570 10.1107/S0021889805008277 (Pubitemid 40830774)
13. Turning protein crystallisation from an art into a science. NE Chayen, Curr Opin Struct Biol 2004 14 577 583 10.1016/j.sbi.2004.08.002 15465318 (Pubitemid 39311821)
14. Life in the fast lane for protein crystallization and X-ray crystallography. M Puesy ZJ Liu W Tempel J Praissman D Lin BC Wang JA Gavira JD Ng, Prog Biophys Mol Biol 2005 88 359 386 10.1016/j.pbiomolbio.2004.07.011 15652250 (Pubitemid 40084821)
15. Predictive models for protein crystallization. B Rupp JW Wang, Methods 2004 34 391 408 10.1016/j.ymeth.2004.03.031 (Pubitemid 39119820)
16. Protein isoelectric point as a predictor for increased crystallization screening efficiency. KA Kantardjieff B Rupp, Bioinformatics 2004 20 2162 2168 10.1093/bioinformatics/bth066 14871873 (Pubitemid 39341602)
17. Distributions of pI vs pH provide strong prior information for the design of crystallization screening experiments. KA Kantardjieff M Jamshidian B Rupp, Bioinformatics 2004 20 2171 2174 10.1093/bioinformatics/bth453
18. Protein biophysical properties that correlate with crystallisation success in Thermotoga maritima: maximum clustering strategy for structural genomics. JM Canaves R Page IA Wilson RC Stevens, J Mol Biol 2004 344 977 991 10.1016/j.jmb.2004.09.076 15544807 (Pubitemid 39491244)
19. Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analyses. CS Goh N Lan SM Douglas B Wu N Echols A Smith D Milburn GT Montelione H Zhao M Gerstein, J Mol Biol 2004 336 115 130 10.1016/j.jmb.2003.11.053 14741208 (Pubitemid 38102334)
20. Will my protein crystallize? A sequence-based predictor. P Smialowski T Schmidt J Cox A Kirschner D Frishman, Proteins 2006 62 343 355 10.1002/prot.20789 16315316 (Pubitemid 43054356)
21. A normalised scale for structural genomics target ranking: the OB-Score. IM Overton GJ Barton, FEBS Lett 2006 580 4005 4009 10.1016/j.febslet.2006.06.015 16808918 (Pubitemid 43946876)
22. Prediction of protein crystallization using collocation of amino acid pairs. K Chen L Kurgan M Rahbari, Biochem Biophys Res Commun 2007 355 764 769 10.1016/j.bbrc.2007.02.040 17316561 (Pubitemid 46330218)
23. ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. IM Overton G Padovani MA Girolami GJ Barton, Bioinformatics 2008 24 901 907 10.1093/bioinformatics/btn055 18285371
24. The challenge of protein structure determination lessons from structural genomics. L Slabinski L Jaroszewski APC Rodrigues L Rychlewski IA Wilson SA Lesley A Godzik, Protein Science 2007 16 11 2472 82 10.1110/ps.073037907 17962404 (Pubitemid 350036752)
25. TargetDB: a target registration database for structural genomics projects. L Chen R Oughtred HM Berman J Westbrook, Bioinformatics 2004 20 16 2860 2 10.1093/bioinformatics/bth300 15130928 (Pubitemid 39530181)
26. Sequence-only based prediction of -turn location and type using collocation of amino acid pairs. K Campbell L Kurgan, Open Bioinf J 2008 2 37 49 10.2174/1875036200802010037
27. Prediction of flexible/rigid regions in proteins from sequences using collocated amino acid pairs. K Chen L Kurgan J Ruan, BMC Struct Biol 2007 7 25 10.1186/1472-6807-7-25 17437643 (Pubitemid 46938033)
28. Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. K Chen Y Jiang L Du L Kurgan, Comput Chem 2009 30 1 163 172 10.1002/jcc.21053
29. Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. YZ Chen YR Tang ZY Sheng Z Zhang, BMC Bioinformatics 2008 9 101 10.1186/1471-2105-9-101 18282281
30. Recent progresses in protein subcellular location prediction. KC Chou HB Shen, Anal Biochem 2007 370 1 16 10.1016/j.ab.2007.07.006 17698024 (Pubitemid 47404494)
31. Progress in protein structural class prediction and its impact to bioinformatics and proteomics. KC Chou, Cur Prot Pept Science 2005 6 423 436 10.2174/138920305774329368 (Pubitemid 41448344)
32. Structural bioinformatics and its impact to biomedical science. KC Chou, Cur Med Chem 2004 11 2105 2134
33. Sequence-based methods for real value predictions of protein structure. LA Kurgan KJ Cios H Zhang T Zhang K Chen S Shen J Ruan, Cur Bioinformatics 2008 3 3 183 196 10.2174/157489308785909197
34. Pattern recognition methods for protein functional site prediction. ZR Yang L Wang N Young KC Chou, Cur Prot Pept Science 2005 6 479 491 10.2174/138920305774329322 (Pubitemid 41448349)
35. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. W Li A Godzik, Bioinformatics 2006 22 1658 1659 10.1093/bioinformatics/btl158 16731699 (Pubitemid 43985301)
36. A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. GJ Barton MJE Sternberg, J Mol Biol 1987 198 327 337 10.1016/0022-2836(87)90316-0 3430611 (Pubitemid 18007540)
37. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. L Goldschmidt DR Cooper Z Derewenda D Eisenberg, Protein Sci 2007 16 1569 76 10.1110/ps.072914007 17656576 (Pubitemid 47195684)
38. Protein identification and analysis tools on the ExPASy server. E Gasteiger C Hoogland A Gattiker S Duvaud MR Wilkins RD Appel A Bairoch, The Proteomics Protocols Handbook Humana Press, Walker JM, 2005 571 607
39. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. B Bjellqvist B Basse E Olsen JE Celis, Electrophoresis 1994 15 529 539 10.1002/elps.1150150171 8055880
40. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. DM Engelman TA Steitz A Goldman, Ann Rev Biophys Biophys Chem 1986 15 321 353 10.1146/annurev.bb.15.060186.001541
41. M Hall, Correlation based feature selection for machine learning, Ph.D. dissertation University of Waikato, Dept of Computer Science 1999
42. Fast learning in networks of locally-tuned processing units. J Moody Ch Darken, Neural Computation 1989 1 281 294 10.1162/neco.1989.1.2.281
43. Normalized Gaussian Radial Basis Function networks. G Bugmann, Neurocomputing 1998 20 97 110 10.1016/S0925-2312(98)00027-7 (Pubitemid 28423529)
44. I Witten E Frank, Data Mining: Practical Machine Learning Tools and Techniques Morgan Kaufmann, San Francisco second 2005
45. XtalPred: a web server for prediction of protein crystallizability. L Slabinski L Jaroszewski L Rychlewski IA Wilson SA Lesley A Godzik, Bioinformatics 2007 23 24 3403 5 10.1093/bioinformatics/btm477 17921170 (Pubitemid 350238899)
46. Protein crystallization by surface entropy reduction: optimization of the SER strategy. DR Cooper T Boczek K Grelewska M Pinkowska M Sikorska M Zawadzki Z Derewenda, Acta Crystallogr D Biol Crystallogr 2007 63 636 45 10.1107/S0907444907010931 17452789 (Pubitemid 46661535)
47. Rational protein crystallization by mutational surface engineering. Z Derewenda, Structure 2004 12 529 35 10.1016/j.str.2004.03.008 15062076 (Pubitemid 38447156)
48. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange Site-Directed Mutagenesis. W Wang BA Malcolm, Biotechniques 1999 26 680 2 10343905