Structure prediction for CASP8 with all-atom refinement using Rosetta

By Srivatsan Raman, Robert M. Vernon, James M. Thompson, Michael D. Tyka, Ruslan I. Sadreyev, Jimin Pei, David E. Kim, Elizabeth H. Kellogg, Frank DiMaio, Oliver F. Lange and 6 more. 2009

496 citations recorded by the source corpus.

We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all‐atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all‐atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template‐based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy. Proteins 2009. © 2009 Wiley‐Liss, Inc.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “ 0 50 100 150 200 0 5 10 15 20 25 30 35 40 SCA rank M in a to m d is ta nc e PCBP1_HUMAN 0 50 100 150 200 0 5 10 15 20 25 30 35 40 SCA rank M in a to m d is ta nc e BPT1_BOVIN 0 50 100 150 200 0 5 10 15 20 25 30 35 40 SCA rank M in a to m d is ta nc e YES_HUMAN 4 Figure S15.”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, methodology): “…side-chains are represented by fixed center-of-mass atoms allowing for rapid generation and evaluation of various protein-like topologies; the second stage (‘full-atom’) builds in explicit side-chains and carries out all atom energy minimization ( Simons et al., 1999 ; Raman et al., 2009 ).”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “Predict the structure of a protein from its sequence (Bonneau et al. , 2001, 2002; Bradley et al. , 2005; Das et al. , 2007; Raman et al. , 2009; Simons et al. , 1997) enzdes Design a protein active site to catalyze a chemical reaction ( Jiang et al. , 2008; Rothlisberger et al. , 2008; Zanghellini…”
High resolution comparative modeling with RosettaCM (2013, methodology): “Previous comparative modeling efforts in Rosetta(Raman et al., 2009; Thompson and Baker, 2011) produced accurate models in some cases, but were unable to combine structural information from multiple templates.”
Large-scale determination of previously unsolved protein structures using evolutionary information (2015, methodology): “…structures of proteins from large families with no representatives of known structure by integrating co-evolution derived contact information from GREMLIN ( Kamisetty et al., 2013 ) into the Rosetta structure prediction methodology ( Simons et al., 1999 ; Rohl et al., 2004 ; Raman et al., 2009 ).”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “These 18 servers are BAKER- ROSETTASERVER (Raman et al., 2009), chunk-TASSER (Zhou et al., 2009), chuo-fams (Kanou et al., 2009), CLEF-Server (Shao et al., 2011), FAMSD (Kanou et al., 2009), gws (Joo et al., 2009), HHpredA (Hildebrand et al., 2009), Jiang_Assembly (Hu et al., 2011), MULTICOM-CLUSTER”
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling (2013, neutral): “33”
Chemical shift-based methods in NMR structure determination (2018, methodology): “Classical methods, including MODELLER [101], I-TASSER [55] and threading protocols in Rosetta [102], have achieved success in performing homology (also referred to as comparative or template-based) modeling even when the similarity between the query and template sequences is low (up to 20–25%) [103]”
Better together: Elements of successful scientific software development in a distributed collaborative community (2020, methodology): “The Robetta server[54] was deployed in 2003 and is commonly used by scientists inside and outside of our community for fragment generation[55], domain parsing and structure prediction[56,57], alanine scanning[58], and DNA interface scanning[59].”
The dual role of fragments in fragment-assembly methods for de novo protein structure prediction (2011, background): “18 Rosetta comprises two key protocols.”
Protein model discrimination using mutational sensitivity derived from deep sequencing. (2012, methodology): “Each of these models was further refined using the Rosetta refinement protocol (Raman et al., 2009) to generate 300–500 models per alignment (see Experimental Procedures).”
CASP9 Assessment of Free Modeling Target Predictions (2011, background): “The known ab initio method Rosetta developed by the Baker group, which has not changed in a significant way since CASP8, provided the most outstanding prediction (prediction 321_4 for target T0581) in CASP9.”
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4* (2015, background): “In the initial stage (“centroid”), side chains are represented by fixed center-of-mass atoms allowing for rapid generation and evaluation of various protein-like topologies; the second stage (“fullatom”) places all-atom side chains into a starting topology and iteratively refines the model until a l”
Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability (2014, methodology): “We applied Rosetta ab initio structure prediction 25 to each designed sequence and each native sequence.”
Assessment of Refinement of Template-Based Models in CASP11 (2016, methodology): “These methods may be more computationally efficient, and optimize the structure by making local changes to reduce the energy of the model.14 The refinement of protein structure models was introduced as a separate category in CASP8 in 200815 and was run in CASP916 and CASP1017 as well as CASP11.”