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David baker rosetta

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https://www.readbyqxmd.com/read/28973862/de-novo-design-of-covalently-constrained-mesosize-protein-scaffolds-with-unique-tertiary-structures
#1
Bobo Dang, Haifan Wu, Vikram Khipple Mulligan, Marco Mravic, Yibing Wu, Thomas Lemmin, Alexander Ford, Daniel-Adriano Silva, David Baker, William F DeGrado
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature...
September 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28940798/protein-structure-prediction-using-rosetta-in-casp12
#2
Sergey Ovchinnikov, Hahnbeom Park, David Kim, Frank DiMaio, David Baker
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure-our model database thus starts to fulfill one of the goals of the original protein structure initiative...
September 22, 2017: Proteins
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#3
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#4
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#5
Rebecca F Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram K Mulligan, Kalli Kappel, Jason W Labonte, Michael S Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15)...
May 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28104891/protein-structure-determination-using-metagenome-sequence-data
#6
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank...
January 20, 2017: Science
https://www.readbyqxmd.com/read/27940918/computational-design-of-a-homotrimeric-metalloprotein-with-a-trisbipyridyl-core
#7
Jeremy H Mills, William Sheffler, Maraia E Ener, Patrick J Almhjell, Gustav Oberdorfer, José Henrique Pereira, Fabio Parmeggiani, Banumathi Sankaran, Peter H Zwart, David Baker
Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3](2+) complexes at the interface between monomers...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27766851/simultaneous-optimization-of-biomolecular-energy-functions-on-features-from-small-molecules-and-macromolecules
#8
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking have been parametrized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
December 13, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26857542/structure-prediction-using-sparse-simulated-noe-restraints-with-rosetta-in-casp11
#9
Sergey Ovchinnikov, Hahnbeom Park, David E Kim, Yuan Liu, Ray Yu-Ruei Wang, David Baker
In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol. Low resolution models were generated guided by the unambiguous restraints using continuous chain folding for alpha and alpha-beta proteins, and iterative annealing for all beta proteins to take advantage of the strand pairing information implicit in the restraints. 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 ambiguous restraints...
September 2016: Proteins
https://www.readbyqxmd.com/read/26374198/engineering-of-kuma030-a-gliadin-peptidase-that-rapidly-degrades-immunogenic-gliadin-peptides-in-gastric-conditions
#10
Clancey Wolf, Justin B Siegel, Christine Tinberg, Alessandra Camarca, Carmen Gianfrani, Shirley Paski, Rongjin Guan, Gaetano Montelione, David Baker, Ingrid S Pultz
Celiac disease is characterized by intestinal inflammation triggered by gliadin, a component of dietary gluten. Oral administration of proteases that can rapidly degrade gliadin in the gastric compartment has been proposed as a treatment for celiac disease; however, no protease has been shown to specifically reduce the immunogenic gliadin content, in gastric conditions, to below the threshold shown to be toxic for celiac patients. Here, we used the Rosetta Molecular Modeling Suite to redesign the active site of the acid-active gliadin endopeptidase KumaMax...
October 14, 2015: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26335199/large-scale-determination-of-previously-unsolved-protein-structures-using-evolutionary-information
#11
Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E Kim, Hetunandan Kamisetty, Nick V Grishin, David Baker
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available...
2015: ELife
https://www.readbyqxmd.com/read/26226626/improving-the-catalytic-performance-of-an-artificial-metalloenzyme-by-computational-design
#12
Tillmann Heinisch, Michela Pellizzoni, Marc Dürrenberger, Christine E Tinberg, Valentin Köhler, Juliane Klehr, Daniel Häussinger, David Baker, Thomas R Ward
Artifical metalloenzymes combine the reactivity of small molecule catalysts with the selectivity of enzymes, and new methods are required to tune the catalytic properties of these systems for an application of interest. Structure-based computational design could help to identify amino acid mutations leading to improved catalytic activity and enantioselectivity. Here we describe the application of Rosetta Design for the genetic optimization of an artificial transfer hydrogenase (ATHase hereafter), [(η(5)-Cp*)Ir(pico)Cl] ⊂ WT hCA II (Cp* = Me5C5(-)), for the asymmetric reduction of a cyclic imine, the precursor of salsolsidine...
August 19, 2015: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26205421/casp11-refinement-experiments-with-rosetta
#13
Hahnbeom Park, Frank DiMaio, David Baker
We report new Rosetta-based approaches to tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment. Automated refinement protocols were developed that integrate a range of sampling methods using parallel computation and multiobjective optimization. In CASP11, we used a more aggressive large-scale structure rebuilding approach for poor starting models, and a less aggressive local rebuilding plus core refinement approach for starting models likely to be closer to the native structure...
September 2016: Proteins
https://www.readbyqxmd.com/read/25971965/computation-and-functional-studies-provide-a-model-for-the-structure-of-the-zinc-transporter-hzip4
#14
Sagar Antala, Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker, Robert E Dempski
Members of the Zrt and Irt protein (ZIP) family are a central participant in transition metal homeostasis as they function to increase the cytosolic concentration of zinc and/or iron. However, the lack of a crystal structure hinders elucidation of the molecular mechanism of ZIP proteins. Here, we employed GREMLIN, a co-evolution-based contact prediction approach in conjunction with the Rosetta structure prediction program to construct a structural model of the human (h) ZIP4 transporter. The predicted contact data are best fit by modeling hZIP4 as a dimer...
July 17, 2015: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/25866491/combined-covalent-electrostatic-model-of-hydrogen-bonding-improves-structure-prediction-with-rosetta
#15
Matthew J O'Meara, Andrew Leaver-Fay, Michael D Tyka, Amelie Stein, Kevin Houlihan, Frank DiMaio, Philip Bradley, Tanja Kortemme, David Baker, Jack Snoeyink, Brian Kuhlman
Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics...
February 10, 2015: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/25707030/atomic-accuracy-models-from-4-5-%C3%A3-cryo-electron-microscopy-data-with-density-guided-iterative-local-refinement
#16
Frank DiMaio, Yifan Song, Xueming Li, Matthias J Brunner, Chunfu Xu, Vincent Conticello, Edward Egelman, Thomas Marlovits, Yifan Cheng, David Baker
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method...
April 2015: Nature Methods
https://www.readbyqxmd.com/read/25700516/transition-states-trapping-a-transition-state-in-a-computationally-designed-protein-bottle
#17
Aaron D Pearson, Jeremy H Mills, Yifan Song, Fariborz Nasertorabi, Gye Won Han, David Baker, Raymond C Stevens, Peter G Schultz
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl...
February 20, 2015: Science
https://www.readbyqxmd.com/read/25587134/the-nmr-rosetta-capsid-model-of-m13-bacteriophage-reveals-a-quadrupled-hydrophobic-packing-epitope
#18
Omry Morag, Nikolaos G Sgourakis, David Baker, Amir Goldbourt
Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16...
January 27, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25451037/a-general-computational-approach-for-repeat-protein-design
#19
Fabio Parmeggiani, Po-Ssu Huang, Sergey Vorobiev, Rong Xiao, Keunwan Park, Silvia Caprari, Min Su, Jayaraman Seetharaman, Lei Mao, Haleema Janjua, Gaetano T Montelione, John Hunt, David Baker
Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability...
January 30, 2015: Journal of Molecular Biology
https://www.readbyqxmd.com/read/25388768/a-hybrid-nmr-saxs-based-approach-for-discriminating-oligomeric-protein-interfaces-using-rosetta
#20
Paolo Rossi, Lei Shi, Gaohua Liu, Christopher M Barbieri, Hsiau-Wei Lee, Thomas D Grant, Joseph R Luft, Rong Xiao, Thomas B Acton, Edward H Snell, Gaetano T Montelione, David Baker, Oliver F Lange, Nikolaos G Sgourakis
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology-based methods, protein-protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet-V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1...
February 2015: Proteins
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