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Casp9 Abstract Book CASP9 ABSTRACT BOOK Critical Assessment of Techniques for Protein Structure Prediction Ninth Meeting PACIFIC GROVE, CALIFORNIA, USA DECEMBER 5-9, 2010 TABLE OF CONTENT 3D-JIGSAW-4.0 .................................................................................................................... 15 3D-JIGSAW-4.5 .................................................................................................................... 15 3D-JIGSAW-4.0 & 3D-JIGSAW-4.5 ....................................................................................................................... 15 3DLIGANDSITE1-4 ................................................................................................................ 17 Using 3DLigandSite to making binding site predictions in CASP9 ....................................................................... 17 3SP-TSAILAB ........................................................................................................................ 19 A side-chain centric method for template-based structure prediction ............................................................... 19 4_BODY_POTENTIALS .......................................................................................................... 21 CASP9: Four Body Potentials for the Prediction of Protein Structure .................................................................. 21 ALADEGAP .......................................................................................................................... 23 Improvement of the Quality of Model Structures by Improving the Template-Target Alignments .................... 23 AOBA .................................................................................................................................. 25 Quality Assessment by Structural Consensus and Statistical Scoring Functions and Modeling by Hybridization of Server Models ................................................................................................................................................. 25 ATOME2_CBS ...................................................................................................................... 27 BAKER ................................................................................................................................. 29 Modeling of Protein Structures Using Rosetta in CASP9 ..................................................................................... 29 BALTYMUS .......................................................................................................................... 31 Quality assesment of single protein structure models using geometrical and statistical techniques ................. 31 BHAGEERATH ...................................................................................................................... 32 Bhageerath: an energy based web-enabled computer software suite for predicting the tertiary structures of soluble proteins ................................................................................................................................................... 32 BHAGEERATH_SCFBIO ......................................................................................................... 34 Bhageerath-H: An ab-initio, homology combined hybrid model for protein tertiary structure prediction ......... 34 BILAB-ENABLE ..................................................................................................................... 36 BILAB-SOLO ......................................................................................................................... 36 BILAB .................................................................................................................................. 36 2 Tertiary Structure Prediction by Combination of Fold Recognition, Realignment, Fragment Assembly and Consensus-based Model Quality Prediction ........................................................................................................ 36 BIO_ICM .............................................................................................................................. 38 Protein structure modeling using 3D-Jury and pyROSETTA ................................................................................ 38 BIOMINE ............................................................................................................................. 40 Prediction of Disorder Regions by Multilayer Information Fusion ...................................................................... 40 BIOSERF .............................................................................................................................. 42 Server-based de novo and fold recognition predictions using BioSerf ................................................................ 42 BUJNICKI-KOLINSKI .............................................................................................................. 43 Protein structure prediction by CABS and TRACER with restraints derived from MQAP-scored models. ........... 43 CBRC_POODLE ..................................................................................................................... 45 POODLE-I: Prediction of disordered region by integrating .................................................................................. 45 POODLE series based on workflow approach ..................................................................................................... 45 CHICKEN_GEORGE ............................................................................................................... 47 Protein structure prediction with SimFold in CASP9............................................................................................ 47 CHUO-FAMS ........................................................................................................................ 49 Construction of the Function for Protein Structure Prediction and the Homology Modeling System ................. 49 CHUNK-TASSER ................................................................................................................... 52 Chunk-TASSER server for protein structure prediction in CASP9 ......................................................................... 52 CIRCLE ................................................................................................................................. 54 Template based modeling server with Model Quality Assessment Program circle ............................................ 54 CNIO ................................................................................................................................... 55 Using predicted contacts to select model structures .......................................................................................... 55 CONFUZZ ............................................................................................................................. 57 ConFuzz residue-residue proximity prediction metaserver ................................................................................. 57 CONQUASS .......................................................................................................................... 59 ConQuass: using evolutionary conservation for quality assessment of protein model structures ...................... 59 CPU_HSFANG ...................................................................................................................... 61 Identification of native-like protein structures among sets of decoys employing a novel average measures approach ............................................................................................................................................................. 61 3 DCLAB ................................................................................................................................. 63 Combining Spectral Analysis with Motif Search and Homology Modeling for Protein Structure Prediction ...... 63 DILL ..................................................................................................................................... 65 Physics-Based Structure Prediction by Zipping and Assembly ............................................................................ 65 DISTILL ................................................................................................................................ 66 DISTILL_HUMAN .................................................................................................................. 66 Distill: protein structure prediction by Machine Learning ................................................................................... 66 DISTILL_NNPIF ..................................................................................................................... 68 DOKHLAB ............................................................................................................................ 69 Protein Structure Prediction by Ab Initio Folding using Discrete Molecular Dynamics ....................................... 69 ELOFSSON ........................................................................................................................... 70 PCONS ................................................................................................................................. 70 PCOMB ............................................................................................................................... 70 PROQ .................................................................................................................................
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