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Capturing expert knowledge with argumentation: a case study in bioinformatics.

Jefferys BR, Kelley LA, Sergot MJ, Fox J, Sternberg MJ.

Bioinformatics. 2006 Apr 15;22(8):924-33. Epub 2006 Jan 29.


PrDOS: prediction of disordered protein regions from amino acid sequence.

Ishida T, Kinoshita K.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W460-4. Epub 2007 Jun 12.


QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.

Suhrer SJ, Gruber M, Sippl MJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W411-5. Epub 2007 May 3.


I-TASSER server for protein 3D structure prediction.

Zhang Y.

BMC Bioinformatics. 2008 Jan 23;9:40. doi: 10.1186/1471-2105-9-40.


Tools for integrated sequence-structure analysis with UCSF Chimera.

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE.

BMC Bioinformatics. 2006 Jul 12;7:339.


Automated discovery of 3D motifs for protein function annotation.

Polacco BJ, Babbitt PC.

Bioinformatics. 2006 Mar 15;22(6):723-30. Epub 2006 Jan 12.


Protein classification using ontology classification.

Wolstencroft K, Lord P, Tabernero L, Brass A, Stevens R.

Bioinformatics. 2006 Jul 15;22(14):e530-8.


SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.


Rapid knot detection and application to protein structure prediction.

Khatib F, Weirauch MT, Rohl CA.

Bioinformatics. 2006 Jul 15;22(14):e252-9.


3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.

Lesk VI, Sternberg MJ.

Bioinformatics. 2008 May 1;24(9):1137-44. doi: 10.1093/bioinformatics/btn093. Epub 2008 Mar 7.


Ensemble classifier for protein fold pattern recognition.

Shen HB, Chou KC.

Bioinformatics. 2006 Jul 15;22(14):1717-22. Epub 2006 May 3.


Modeling protein loops with knowledge-based prediction of sequence-structure alignment.

Peng HP, Yang AS.

Bioinformatics. 2007 Nov 1;23(21):2836-42. Epub 2007 Sep 7.


Identification of function-associated loop motifs and application to protein function prediction.

Espadaler J, Querol E, Aviles FX, Oliva B.

Bioinformatics. 2006 Sep 15;22(18):2237-43. Epub 2006 Jul 26.


POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions.

Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T.

Bioinformatics. 2007 Aug 15;23(16):2046-53. Epub 2007 Jun 1.


Identification of Intrinsically Unstructured Proteins using hierarchical classifier.

Yang JY, Yang MQ.

Int J Data Min Bioinform. 2008;2(2):121-33.


Classification of small molecules by two- and three-dimensional decomposition kernels.

Ceroni A, Costa F, Frasconi P.

Bioinformatics. 2007 Aug 15;23(16):2038-45. Epub 2007 Jun 5.


Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments.

McGuffin LJ, Roche DB.

Bioinformatics. 2010 Jan 15;26(2):182-8. doi: 10.1093/bioinformatics/btp629. Epub 2009 Nov 6.


OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.

Viklund H, Elofsson A.

Bioinformatics. 2008 Aug 1;24(15):1662-8. doi: 10.1093/bioinformatics/btn221. Epub 2008 May 12.

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