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Multipass membrane protein structure prediction using Rosetta

Vladimir Yarov-Yarovoy, Jack Schonbrun, David Baker
2005 Proteins: Structure, Function, and Bioinformatics  
We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures.  ...  Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue  ...  IV Membrane Proteins Tested Using Rosetta-Membrane Method No.  ... 
doi:10.1002/prot.20817 pmid:16372357 pmcid:PMC1479309 fatcat:nkmbgxcbyjclzierjexoah43ty

Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13 [article]

Georg Kuenze, Jens Meiler
2019 bioRxiv   pre-print
We describe our approach to predict the structure of these proteins leveraging the Rosetta software suite. Protein structure models were predicted de novo using a two-stage protocol.  ...  structure prediction.  ...  Montelione and the members of his group for preparing NMR data and assessing predictions, and the structural biologists who generously provided structure targets.  ... 
doi:10.1101/597724 fatcat:zfb3x66lnvafrpnj3lp5w4znru

Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta

Jad Abbass, Jean-Christophe Nebel
2017 Protein Peptide Letters  
Protein structure prediction is considered a main challenge in computational biology.  ...  Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction.  ...  predictions involved in this study.  ... 
doi:10.2174/0929866523666161216124019 pmid:27993124 fatcat:l7iv7etombaxvmc7frym5jh6jq

Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA

C. Bystroff, Y. Shao
2002 Bioinformatics  
Results: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment.  ...  Motivation: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and  ...  P(ss | i) = q γ (q | i)P(ss | q). (1) Rosetta: a conformational search algorithm for proteins Rosetta searches protein conformational space using fragment insertion moves and a Monte Carlo acceptance  ... 
doi:10.1093/bioinformatics/18.suppl_1.s54 pmid:12169531 fatcat:4s25unnsv5cddoyzftlk26o4ba

Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14

Ivan Anishchenko, Minkyung Baek, Hahnbeom Park, Naozumi Hiranuma, David E. Kim, Justas Dauparas, Sanaa Mansoor, Ian R. Humphreys, David Baker
2021 Proteins: Structure, Function, and Bioinformatics  
The trRosetta structure prediction method employs deep learning to generate predicted residue-residue distance and orientation distributions from which 3D models are built.  ...  We also used the DeepAccNet accuracy predictor to guide Rosetta high-resolution refinement for submissions in the regular and refinement categories; although performance was quite good on a CASP relative  ...  distance signed error (represented as histograms of residue-pair distance errors, or estogram in short) in protein models and can be used to guide Rosetta protein structure refinement.  ... 
doi:10.1002/prot.26194 pmid:34331359 pmcid:PMC8616808 fatcat:osgenxfqlzbqlm5ksmbvvacydi

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11

Sergey Ovchinnikov, Hahnbeom Park, David E. Kim, Yuan Liu, Ray Yu-Ruei Wang, David Baker
2016 Proteins: Structure, Function, and Bioinformatics  
In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol.  ...  The Rosetta fragment/model hybridization protocol was then used to recombine and regularize these models, and refine them in the Rosetta full atom energy function guided by both the unambiguous and the  ...  Acknowledgments Authors thank Keith Laidig and Darwin Alonso for developing the computational and network infrastructure and Rosetta@home participants for providing the computing resources necessary for  ... 
doi:10.1002/prot.25006 pmid:26857542 pmcid:PMC5490372 fatcat:zasgvqv5trfs7k3uvd6f5jl24i

Structure prediction for CASP8 with all-atom refinement using Rosetta

Srivatsan Raman, Robert Vernon, James Thompson, Michael Tyka, Ruslan Sadreyev, Jimin Pei, David Kim, Elizabeth Kellogg, Frank DiMaio, Oliver Lange, Lisa Kinch, Will Sheffler (+4 others)
2009 Proteins: Structure, Function, and Bioinformatics  
We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction.  ...  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  ...  They also thank Patrick Barth, Ian Davis, Andrew Leaver-Fay, Hua Cheng, and Yong Wang for help with predictions.  ... 
doi:10.1002/prot.22540 pmid:19701941 pmcid:PMC3688471 fatcat:e23ndynfpvg6vjcaa4frrpm7hi

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

Rhiju Das, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D. Tyka, Divya Bhat, Dylan Chivian, David E. Kim, William H. Sheffler (+5 others)
2007 Proteins: Structure, Function, and Bioinformatics  
of all-atom refinement extensive sampling improves over templates accurate de novo prediction (RMSD<0.2nm) Limitations method does not converge for longer proteins ruggedness of all-atom energy landscape  ...  CASP8 anticipation (http://boincstats.com/) Loop modeling with constrained all-atom refinement full chain refinement + 3D Jury distance constrains 3 Iterative segment rebuilding and all-atom refinement Usefulness  ... 
doi:10.1002/prot.21636 pmid:17894356 fatcat:xtc77clqyffjzio5wuzoqbwkie

Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application

Stephanie S. Kim, Justin T. Seffernick, Steffen Lindert
2018 Journal of Physical Chemistry B  
Using 245 proteins from a benchmark dataset (16 DisProt database proteins) and a test dataset (229 proteins with NMR data), we use Rosetta to predict the global protein structures and then show that there  ...  Here we introduce a user-friendly and reliable approach for the prediction of disordered protein regions using the structure prediction software Rosetta.  ...  Acknowledgments The authors would like to thank the members of the Lindert group for useful discussions.  ... 
doi:10.1021/acs.jpcb.8b01763 pmid:29595057 pmcid:PMC5897131 fatcat:x7bufmmbszcqjd7bp74f6nxuzm

De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds

Yang Shen, Philip N. Bryan, Yanan He, John Orban, David Baker, Ad Bax
2010 Protein Science  
Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods.  ...  Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS-Rosetta structure prediction program and yields adequate convergence, even when input chemical  ...  Acknowledgments The authors thank Rosetta@home participants and the BOINC project for contributing computing power.  ... 
doi:10.1002/pro.303 pmid:19998407 pmcid:PMC2865713 fatcat:767dctts5jeezgyjgwv6gjxssa

Practically Useful: What the RosettaProtein Modeling Suite Can Do for You

Kristian W. Kaufmann, Gordon H. Lemmon, Samuel L. DeLuca, Jonathan H. Sheehan, Jens Meiler
2010 Biochemistry  
ROSETTA has been used to accurately design a novel protein structure, predict the structure of protein-protein complexes, design altered specificity protein-protein and protein-DNA interactions, and stabilize  ...  More impressively, there are several cases in which ROSETTA has been used to predict structures with atomic level accuracy better than 2.5 Å .  ...  ROSETTA is a unified software package for protein structure prediction and functional design.  ... 
doi:10.1021/bi902153g pmid:20235548 pmcid:PMC2850155 fatcat:piiozkxm3fgppnnvksnguadxsa

Prediction of Protein Structure Using Surface Accessibility Data

Christoph Hartlmüller, Christoph Göbl, Tobias Madl
2016 Angewandte Chemie International Edition  
improves accuracy and convergence of the standard Rosetta structure prediction approach.  ...  This method exploits the distance-to-surface information encoded in the sPRE data in the chemical shift-based CS-Rosetta de novo structure prediction framework to generate reliable structural models.  ...  Keywords: CS-Rosetta · NMR spectroscopy · paramagnetic relaxation · protein structure prediction · structural biology  ... 
doi:10.1002/anie.201604788 pmid:27560616 pmcid:PMC5026166 fatcat:wr74g6i4bjfuzikgykkv263qqy

PconsFold: improved contact predictions improve protein models

Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson
2014 Computer applications in the biosciences : CABIOS  
Given sufficiently large protein families, the contact predictions contain sufficient information to predict the structure of many protein families.  ...  Availability: PconsFold is a fully automated pipeline for ab initio protein structure prediction based on evolutionary information.  ...  To optimize protein structure prediction from predicted contacts, we developed PconsFold, a pipeline for ab initio protein structure prediction of single-domain proteins, see Figure 1 .  ... 
doi:10.1093/bioinformatics/btu458 pmid:25161237 pmcid:PMC4147911 fatcat:hpgmw6bdbffa5odjdvhf6kwybe

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta

Ben Blum, Michael I. Jordan, David Kim, Rhiju Das, Philip Bradley, David Baker
2007 Neural Information Processing Systems  
In this paper we present a resampling technique for structure prediction of small alpha/beta proteins using Rosetta.  ...  Rosetta is one of the leading algorithms for protein structure prediction today. It is a Monte Carlo energy minimization method requiring many random restarts to find structures with low energy.  ...  The biological function of a protein is dependent on its structure, so structure prediction is an important step towards function prediction.  ... 
dblp:conf/nips/BlumJKDBB07 fatcat:eknti2s3sbc3ndz6voqsowpus4

Blind tests of RNA–protein binding affinity prediction

Kalli Kappel, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf, Daniel Herschlag, Rhiju Das
2019 Proceedings of the National Academy of Sciences of the United States of America  
of mutations, and use of secondary structure-based energetic calculations to model unbound RNA states.  ...  Here, we bring together several advances to complete a calculation framework for RNA–protein binding affinities, including a unified free energy function for bound complexes, automated Rosetta modeling  ...  *These predictions were made using a PUM1 crystal structure in addition to the three PUM2 crystal structures.  ... 
doi:10.1073/pnas.1819047116 pmid:30962376 pmcid:PMC6486753 fatcat:u4g3yus2a5gzro3iyqd5hbtvra
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