LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction

We present the results of the evaluation of the latest LiveBench‐8 experiment. These results provide a snapshot view of the state of the art in automated protein structure prediction, just before the 2004 CAFASP‐4/CASP‐6 experiments begin. The last CAFASP/CASP experiments demonstrated that automated meta‐predictors entail a significant advance in the field, already challenging most human expert predictors. LiveBench‐8 corroborates the superior performance of meta‐predictors, which are able to produce useful predictions for over one‐half of the test targets. More importantly, LiveBench‐8 identifies a handful of recently developed autonomous (nonmeta) servers that perform at the very top, suggesting that further progress in the individual methods has recently been obtained.

[1]  Roland L. Dunbrack,et al.  CAFASP3: The third critical assessment of fully automated structure prediction methods , 2003, Proteins.

[2]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[3]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[4]  Arne Elofsson,et al.  MaxSub: an automated measure for the assessment of protein structure prediction quality , 2000, Bioinform..

[5]  D Fischer,et al.  The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2. , 2000, Protein engineering.

[6]  David Baker,et al.  We need both computer models and experiments , 2001, Nature.

[7]  Arne Elofsson,et al.  3D-Jury: A Simple Approach to Improve Protein Structure Predictions , 2003, Bioinform..

[8]  Eaton E Lattman,et al.  Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction , 2007, Proteins.

[9]  Daniel Fischer,et al.  3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor , 2003, Proteins.

[10]  A. Godzik,et al.  Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.

[11]  Jakub Pas,et al.  The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries , 2004, Bioinform..

[12]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[13]  Kevin Karplus,et al.  Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set , 2001, Bioinform..

[14]  Volker A. Eyrich,et al.  EVA: Large‐scale analysis of secondary structure prediction , 2001, Proteins.

[15]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[16]  Alison Abbott,et al.  Computer modellers seek out 'Ten Most Wanted' proteins , 2001, Nature.

[17]  D Fischer,et al.  Hybrid fold recognition: combining sequence derived properties with evolutionary information. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[18]  Liam J. McGuffin,et al.  Improvement of the GenTHREADER Method for Genomic Fold Recognition , 2003, Bioinform..

[19]  Hidetoshi Kono,et al.  Anatomy of specific interactions between λ repressor and operator DNA , 2003 .

[20]  J Lundström,et al.  Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.

[21]  L Rychlewski,et al.  Fold predictions for bacterial genomes. , 2001, Journal of structural biology.

[22]  D Fischer,et al.  LiveBench‐1: Continuous benchmarking of protein structure prediction servers , 2001, Protein science : a publication of the Protein Society.

[23]  M. Sternberg,et al.  Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.

[24]  D. Fischer,et al.  The 2002 Olympic Games of protein structure prediction. , 2003, Protein Engineering.

[25]  D. Fischer,et al.  Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[26]  E. Lattman,et al.  Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction , 2022 .