CRITICAL ASSESSMENT OF TECHNIQUES FOR PROTEIN STRUCTURE PREDICTION 13 Thirteenth meeting Riviera Maya, Mexico DECEMBER 1-4, 2018 1 TABLE OF CONTENTS 3DCNN (TS) .......................................................................................................................................................................... 9 PROTEIN MODEL QUALITY ASSESSMENT USING 3D ORIENTED CONVOLUTIONAL NEURAL NETWORK ................................................................ 9 3DCNN (REFINEMENT) ....................................................................................................................................................... 10 REFINEMENT OF PROTEIN MODELS WITH ADDITIONAL CROSS-LINKING INFORMATION USING THE GAUSSIAN NETWORK AND GRADIENT DESCENT .. 10 A7D ................................................................................................................................................................................... 11 DE NOVO STRUCTURE PREDICTION WITH DEEP-LEARNING BASED SCORING.............................................................................................. 11 AIR ..................................................................................................................................................................................... 13 AIR: AN ARTIFICIAL INTELLIGENCE-BASED PROTOCOL FOR PROTEIN STRUCTURE REFINEMENT USING MULTI-OBJECTIVE PARTICLE SWARM OPTIMIZATION ........................................................................................................................................................................... 13 ALPHACONTACT ................................................................................................................................................................. 15 PROTEIN CONTACT PREDICTION WITH MULTI-SCALE RESIDUAL CONVOLUTIONAL NEURAL NETWORK .......................................................... 15 AP_1 .................................................................................................................................................................................. 17 AP_1 STRUCTURE PREDICTION IN CASP13 ..................................................................................................................................... 17 AWSEM-SUITE ................................................................................................................................................................... 18 TEMPLATE-GUIDED & COEVOLUTION-RESTRAINED PROTEIN STRUCTURE PREDICTION USING OPTIMIZED FOLDING LANDSCAPE FORCE FIELDS ... 18 BAKER_AUTOREFINE .......................................................................................................................................................... 20 ADDRESSING MEDIUM-RESOLUTION REFINEMENT CHALLENGES USING ROSETTA IN CASP13 ..................................................................... 20 BAKER-ROSETTASERVER .................................................................................................................................................... 22 IMPROVING ROBETTA BY A BROAD USAGE OF SEQUENCE DATA AND COEVOLUTIONARY RESTRAINTS .............................................................. 22 BATES_BMM ...................................................................................................................................................................... 25 PROTEIN MODEL CONSTRUCTION AND DOCKING USING PARTICLE SWARM OPTIMIZATION ........................................................................... 25 BCLMEILERGROUP ............................................................................................................................................................. 27 BCL::FOLD DE-NOVO PROTEIN STRUCTURE PREDICTION THROUGH ASSEMBLY OF SECONDARY STRUCTURE ELEMENTS FOLLOWED BY MOLECULAR DYNAMICS REFINEMENT ............................................................................................................................................................... 27 BHATTACHARYA ................................................................................................................................................................. 29 PROTEIN STRUCTURE PREDICTION AND REFINEMENT BY BHATTACHARYA HUMAN GROUP IN CASP13 .......................................................... 29 BHATTACHARYA-CLUSTQ .................................................................................................................................................... 31 CLUSTQ: MULTI-MODEL QA USING SUPERPOSITION-FREE WEIGHTED INTERNAL DISTANCE COMPARISONS .................................................... 31 BHATTACHARYA-SERVER .................................................................................................................................................... 32 REFINED: PROTEIN STRUCTURE REFINEMENT USING MACHINE LEARNING GUIDED RESTRAINED RELAXATION .................................................. 32 BHATTACHARYA-SINGQ, BHATTACHARYA-SERVER .............................................................................................................. 33 SCORED: ESTIMATING GLOBAL DISTANCE TEST USING DEEP DISCRIMINATIVE BINARY CLASSIFIER ENSEMBLE .................................................. 33 BONIECKI_PRED ................................................................................................................................................................. 35 PROTEIN STRUCTURE REFINEMENT USING INTERMEDIATE RESOLUTION, COARSE-GRAINED MODEL, KNOWLEDGE-BASED ENERGY FUNCTION(S), MONTE CARLO METHODS, SUPPORTED BY MQAP CONSTRAINTS ......................................................................................................... 35 CAO-SERVER (TS) ............................................................................................................................................................... 36 COLLABORATIVE DE NOVO PROTEIN STRUCTURE PREDICTION USING STEPWISE FRAGMENT SAMPLING WITH HELP OF CONTACT PREDICTION AND MODEL SELECTION BASED ON DEEP LEARNING TECHNIQUES ................................................................................................................. 36 CARBONELAB (CAPRI) ........................................................................................................................................................ 38 2 COMBINING EVOLUTION- AND GEOMETRY-DRIVEN INTERFACE PREDICTIONS WITH KNOWLEDGE-BASED DISTANCE-DEPENDENT POTENTIALS FOR TEMPLATE-FREE MODELING IN CAPRI ROUND 46 ............................................................................................................................. 38 CLUSPRO (CAPRI) ............................................................................................................................................................... 40 HYBRID CLUSPRO SERVER IN 2018 CASP/CAPRI ROUNDS ................................................................................................................ 40 CPCLAB (RR)....................................................................................................................................................................... 42 TOPCONTACT: PROTEIN CONTACT META-PREDICTIONS THROUGH MACHINE LEARNING .............................................................................. 42 CPCLAB (TS) ....................................................................................................................................................................... 43 TOPSCORE: USING DEEP NEURAL NETWORKS AND LARGE DIVERSE DATASETS FOR ACCURATE PROTEIN MODEL QUALITY ASSESSMENT .................. 43 D-HAVEN ........................................................................................................................................................................... 45 TEMPLATE-BASED PROTEIN STRUCTURE PREDICTION BASED ON PROFILE-PROFILE ALIGNMENTS ................................................................ 45 DC_REFINE ......................................................................................................................................................................... 47 MODYCHOPS - MOLECULAR DYNAMICS COUPLED HOMOLOGUE PROTEIN STRUCTURE REFINEMENT PROTOCOL ......................................... 47 DELCLAB ............................................................................................................................................................................ 48 COMBINING ORTHODOX SEQUENCE HOMOLOGY ANALYSIS WITH SPECTRAL ANALYSIS FOR PROTEIN 3D STRUCTURE PREDICTION ........................ 48 DESTINI .............................................................................................................................................................................. 50 A DEEP-LEARNING APPROACH TO PROTEIN STRUCTURE PREDICTION ...................................................................................................... 50 DISTILL ............................................................................................................................................................................... 52 DISTILL FOR CASP13 .................................................................................................................................................................. 52 DL-HAVEN .......................................................................................................................................................................... 54 CONTACT PREDICTION AND DE NOVO PROTEIN STRUCTURE