Wikipedia

Rosetta@home

Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker lab. Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about fifty-five thousand active volunteered computers processing at over 487,946 GigaFLOPS on average as of September 19, 2020.[4] Foldit, a Rosetta@home videogame, aims to reach these goals with a crowdsourcing approach. Though much of the project is oriented toward basic research to improve the accuracy and robustness of proteomics methods, Rosetta@home also does applied research on malaria, Alzheimer's disease, and other pathologies.[5]

Rosetta@home
Developer(s)Baker laboratory, University of Washington; Rosetta Commons
Initial releaseOctober 6, 2005; 19 years ago (2005-10-06)
Stable releaseRosetta: 4.20 / May 1, 2020; 4 years ago (2020-05-01)

Rosetta Mini: 3.78 / October 3, 2017; 7 years ago (2017-10-03)

Rosetta for Android: 4.20 / May 1, 2020; 4 years ago (2020-05-01)
Development statusActive
Operating systemWindows, macOS, Linux, Android
PlatformBOINC
LicenseProprietary freeware for academic and non-profit use[1]
Average performance68,735 GigaFLOPS[2]
Active users11,730
Total users1,381,253[3]
Active hosts23,122
Total hosts4,537,689
Websiteboinc.bakerlab.org/rosetta/

Like all BOINC projects, Rosetta@home uses idle computer processing resources from volunteers' computers to perform calculations on individual workunits. Completed results are sent to a central project server where they are validated and assimilated into project databases. The project is cross-platform, and runs on a wide variety of hardware configurations. Users can view the progress of their individual protein structure prediction on the Rosetta@home screensaver.

In addition to disease-related research, the Rosetta@home network serves as a testing framework for new methods in structural bioinformatics. Such methods are then used in other Rosetta-based applications, like RosettaDock or the Human Proteome Folding Project and the Microbiome Immunity Project, after being sufficiently developed and proven stable on Rosetta@home's large and diverse set of volunteer computers. Two especially important tests for the new methods developed in Rosetta@home are the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and Critical Assessment of Prediction of Interactions (CAPRI) experiments, biennial experiments which evaluate the state of the art in protein structure prediction and protein–protein docking prediction, respectively. Rosetta consistently ranks among the foremost docking predictors, and is one of the best tertiary structure predictors available.[6]

With an influx of new users looking to participate in the fight against the COVID-19 pandemic, caused by SARS-CoV-2, Rosetta@home increased its computing power up to 1.7 PetaFlops as of March 28, 2020.[7][8] On September 9, 2020, Rosetta@home researchers published a paper describing 10 potent antiviral candidates against SARS-CoV-2. Rosetta@home contributed to this research and these antiviral candidates are heading towards Phase 1 clinical trials, which may begin in early 2022.[9][10][11][12] According to the Rosetta@home team, Rosetta volunteers contributed to the development of a nanoparticle vaccine.[9] This vaccine has been licensed and is known as the IVX-411 by Icosavax, which began a Phase I/II clinical trial in June 2021,[13] and GBP510 which is being developed by SK Bioscience and is already approved for a Phase III clinical trial in South Korea.[14][15]

NL-201, a cancer drug candidate that was first created at the Institute of Protein Design (IPD) and published in a January 2019 paper,[16] began a Phase 1 Human clinical trial in May 2021 with the support of Neoleukin Therapeutics, itself a spin-off from the IPD.[17] Rosetta@home played a role in the development of NL-201 and contributed with "forward folding" experiments that helped validate protein designs.[18]

Computing platform

edit
See also: List of volunteer computing projects

The Rosetta@home application and the BOINC volunteer computing platform are available for the operating systems Windows, Linux, and macOS; BOINC also runs on several others, e.g., FreeBSD.[19] Participation in Rosetta@home requires a central processing unit (CPU) with a clock speed of at least 500 MHz, 200 megabytes of free disk space, 512 megabytes of physical memory, and Internet connectivity.[20] As of July 20, 2016, the current version of the Rosetta Mini application is 3.73.[21] The current recommended BOINC program version is 7.6.22.[19] Standard Hypertext Transfer Protocol (HTTP) (port 80) is used for communication between the user's BOINC client and the Rosetta@home servers at the University of Washington; HTTPS (port 443) is used during password exchange. Remote and local control of the BOINC client use port 31416 and port 1043, which might need to be specifically unblocked if they are behind a firewall.[22] Workunits containing data on individual proteins are distributed from servers located in the Baker lab at the University of Washington to volunteers' computers, which then calculate a structure prediction for the assigned protein. To avoid duplicate structure predictions on a given protein, each workunit is initialized with a random seed number. This gives each prediction a unique trajectory of descent along the protein's energy landscape.[23] Protein structure predictions from Rosetta@home are approximations of a global minimum in a given protein's energy landscape. That global minimum represents the most energetically favorable conformation of the protein, i.e., its native state.

 
Rosetta@home screensaver, showing the progress of a structure prediction for a synthetic ubiquitin protein (PDB ID: 1ogw)

A primary feature of the Rosetta@home graphical user interface (GUI) is a screensaver which shows a current workunit's progress during the simulated protein folding process. In the upper-left of the current screensaver, the target protein is shown adopting different shapes (conformations) in its search for the lowest energy structure. Depicted immediately to the right is the structure of the most recently accepted. On the upper right the lowest energy conformation of the current decoy is shown; below that is the true, or native, structure of the protein if it has already been determined. Three graphs are included in the screensaver. Near the middle, a graph for the accepted model's thermodynamic free energy is displayed, which fluctuates as the accepted model changes. A graph of the accepted model's root-mean-square deviation (RMSD), which measures how structurally similar the accepted model is to the native model, is shown far right. On the right of the accepted energy graph and below the RMSD graph, the results from these two functions are used to produce an energy vs. RMSD plot as the model is progressively refined.[24]

Like all BOINC projects, Rosetta@home runs in the background of the user's computer, using idle computer power, either at or before logging into an account on the host operating system. The program frees resources from the CPU as they are needed by other applications so that normal computer use is unaffected. Many program settings can be specified via user account preferences, including: the maximum percentage of CPU resources the program can use (to control power consumption or heat production from a computer running at sustained capacity), the times of day during which the program can run, and many more.[citation needed]

Project significance

edit
Further information: Protein structure prediction, Protein docking, and Protein design

With the proliferation of genome sequencing projects, scientists can infer the amino acid sequence, or primary structure, of many proteins that carry out functions within the cell. To better understand a protein's function and aid in rational drug design, scientists need to know the protein's three-dimensional tertiary structure.

 
CASP6 target T0281, the first ab initio protein structure prediction to approach atomic-level resolution. Rosetta produced a model for T0281 (superpositioned in magenta) 1.5 Ångström (Å) RMSD from the crystal structure (blue).

Protein 3D structures are currently determined experimentally via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The process is slow (it can take weeks or even months to figure out how to crystallize a protein for the first time) and costly (around US$100,000 per protein).[25] Unfortunately, the rate at which new sequences are discovered far exceeds the rate of structure determination – out of more than 7,400,000 protein sequences available in the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database, fewer than 52,000 proteins' 3D structures have been solved and deposited in the Protein Data Bank, the main repository for structural information on proteins.[26] One of the main goals of Rosetta@home is to predict protein structures with the same accuracy as existing methods, but in a way that requires significantly less time and money. Rosetta@home also develops methods to determine the structure and docking of membrane proteins (e.g., G protein–coupled receptors (GPCRs)),[27] which are exceptionally difficult to analyze with traditional techniques like X-ray crystallography and NMR spectroscopy, yet represent the majority of targets for modern drugs.[28]

Progress in protein structure prediction is evaluated in the biannual Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, in which researchers from around the world attempt to derive a protein's structure from the protein's amino acid sequence. High scoring groups in this sometimes competitive experiment are considered the de facto standard-bearers for what is the state of the art in protein structure prediction. Rosetta, the program on which Rosetta@home is based, has been used since CASP5 in 2002. In the 2004 CASP6 experiment, Rosetta made history by being the first to produce a close to atomic-level resolution, ab initio protein structure prediction in its submitted model for CASP target T0281.[29] Ab initio modeling is considered an especially difficult category of protein structure prediction, as it does not use information from structural homology and must rely on information from sequence homology and modeling physical interactions within the protein. Rosetta@home has been used in CASP since 2006, where it was among the top predictors in every category of structure prediction in CASP7.[30][31][32] These high quality predictions were enabled by the computing power made available by Rosetta@home volunteers.[33] Increasing computing power allows Rosetta@home to sample more regions of conformation space (the possible shapes a protein can assume), which, according to Levinthal's paradox, is predicted to increase exponentially with protein length.[citation needed]

Rosetta is also used in protein–protein docking prediction, which determines the structure of multiple complexed proteins, or quaternary structure. This type of protein interaction affects many cellular functions, including antigen–antibody and enzyme–inhibitor binding and cellular import and export. Determining these interactions is critical for drug design. Rosetta is used in the Critical Assessment of Prediction of Interactions (CAPRI) experiment, which evaluates the state of the protein docking field similar to how CASP gauges progress in protein structure prediction. The computing power made available by Rosetta@home's project volunteers has been cited as a major factor in Rosetta's performance in CAPRI 2007, where its docking predictions have been among the most accurate and complete.[34]

In early 2008, Rosetta was used to computationally design a protein with a function never before observed in nature.[35] This was inspired in part by the retraction of a high-profile paper from 2004 which originally described the computational design of a protein with improved enzymatic activity relative to its natural form.[36] The 2008 research paper from David Baker's group describing how the protein was made, which cited Rosetta@home for the computing resources it made available, represented an important proof of concept for this protein design method.[35] This type of protein design could have future applications in drug discovery, green chemistry, and bioremediation.[35]

The Rosetta computer program was cited in the 2024 Scientific Background to the Nobel Prize in Chemistry.[37]

edit

In addition to basic research in predicting protein structure, docking and design, Rosetta@home is also used in immediate disease-related research.[38] Numerous minor research projects are described in David Baker's Rosetta@home journal.[39] As of February 2014, information on recent publications and a short description of the work are being updated on the forum.[40] The forum thread is no longer used since 2016, and news on the research can be found on the general news section of the project.[41]

Alzheimer's disease

edit

A component of the Rosetta software suite, RosettaDesign, was used to accurately predict which regions of amyloidogenic proteins were most likely to make amyloid-like fibrils.[42] By taking hexapeptides (six amino acid-long fragments) of a protein of interest and selecting the lowest energy match to a structure similar to that of a known fibril forming hexapeptide, RosettaDesign was able to identify peptides twice as likely to form fibrils as are random proteins.[43] Rosetta@home was used in the same study to predict structures for amyloid beta, a fibril-forming protein that has been postulated to cause Alzheimer's disease.[44] Preliminary but as yet unpublished results have been produced on Rosetta-designed proteins that may prevent fibrils from forming, although it is unknown whether it can prevent the disease.[45]

Anthrax

edit

Another component of Rosetta, RosettaDock,[46][47][48] was used in conjunction with experimental methods to model interactions between three proteins—lethal factor (LF), edema factor (EF) and protective antigen (PA)—that make up anthrax toxin. The computer model accurately predicted docking between LF and PA, helping to establish which domains of the respective proteins are involved in the LF–PA complex. This insight was eventually used in research resulting in improved anthrax vaccines.[49][50]

Herpes simplex virus 1

edit

RosettaDock was used to model docking between an antibody (immunoglobulin G) and a surface protein expressed by the cold sore virus, herpes simplex virus 1 (HSV-1) which serves to degrade the antiviral antibody. The protein complex predicted by RosettaDock closely agreed with the especially difficult-to-obtain experimental models, leading researchers to conclude that the docking method has potential to address some of the problems that X-ray crystallography has with modelling protein–protein interfaces.[51]

HIV

edit

As part of research funded by a $19.4 million grant by the Bill & Melinda Gates Foundation,[52] Rosetta@home has been used in designing multiple possible vaccines for human immunodeficiency virus (HIV).[53][54]

Malaria

edit

In research involved with the Grand Challenges in Global Health initiative,[55] Rosetta has been used to computationally design novel homing endonuclease proteins, which could eradicate Anopheles gambiae or otherwise render the mosquito unable to transmit malaria.[56] Being able to model and alter protein–DNA interactions specifically, like those of homing endonucleases, gives computational protein design methods like Rosetta an important role in gene therapy (which includes possible cancer treatments).[38][57]

COVID-19

edit

In 2020, the Rosetta molecular modelling suite was used to accurately predict the atomic-scale structure of the SARS-CoV-2 spike protein weeks before it could be measured in the lab.[58] On June 26 of 2020, the project announced it had succeeded in creating antiviral proteins that neutralize SARS-CoV-2 virions in the lab and that these experimental antiviral drugs are being optimized for animal testing trials.[59]

In a follow-up, a paper describing 10 SARS-CoV-2 miniprotein inhibitors was published in Science on September 9. Two of these inhibitors, LCB1 and LCB3, are several times more potent than the best monoclonal antibodies being developed against SARS-CoV-2, both on a molar and mass basis. In addition, the research suggests that these inhibitors retain their activity at elevated temperatures, are 20-fold smaller than an antibody and thus, have 20-fold more potential neutralizing sites, increasing the potential efficacy of a locally administered drug. The small size and high stability of the inhibitors is expected to make them adequate to a gel formulation that can be nasally applied or as a powder to be administered directly onto the respiratory system. The researchers will work on developing these inhibitors into therapeutics and prophylactics in the months ahead.[10] As of July 2021, these antiviral candidates were forecasted to begin clinical trials in early 2022 and had received funding from the Bill & Melinda Gates Foundation for preclinical and early clinical trials.[12] In animal testing trials, these antiviral candidates were effective against variants of concern including Alpha, Beta and Gamma.[12][60][61]

Rosetta@home was used to help screen the over 2 million SARS-CoV-2 Spike-binding proteins that were computationally designed, and thus, contributed to this research.[62][63]

Per the Rosetta@home team at the Institute of Protein Design, Rosetta@home volunteers contributed to the development of antiviral drug candidates[10] and to a protein nanoparticle vaccine.[64] The IVX-411 vaccine is already on a Phase 1 clinical trial run by Icosavax[13] while the same vaccine, licensed to another manufacturer and under the name GBP510, has been approved in South Korea for a Phase III trial run by SK Bioscience.[15][14] The candidate antivirals are also going towards Phase 1 clinical trials.[9]

Cancer

edit
See also: NL-201

Rosetta@home researchers have designed an IL-2 receptor agonist called Neoleukin-2/15 that does not interact with the alpha subunit of the receptor. Such immunity signal molecules are useful in cancer treatment. While the natural IL-2 suffers from toxicity due to an interaction with the alpha subunit, the designed protein is much safer, at least in animal models.[16] Rosetta@home contributed in "forward folding experiments" which helped validate designs.[18]

In a September 2020 feature in the New Yorker, David Baker stated that Neoleukin-2/15 would begin human clinical trials "later this year". Neoleukin-2/15 is being developed by Neoleukin, a spin-off company from the Baker lab.[65] In December 2020, Neoleukin announced it would be submitting an Investigational New Drug application with the Food and Drug Administration in order to begin a Phase 1 clinical trial of NL-201, which is a further development of Neoleukin-2/15. A similar application was submitted in Australia and Neoleukin hopes to enrol up 120 participants on the Phase 1 clinical trial.[66] The Phase 1 human clinical trial began on May 5, 2021.[17]

Rosetta software

edit
Rosetta
Developer(s)Baker laboratory, University of Washington; Rosetta Commons
Initial release1998[67]
Stable release
3.13[68]
Licenseproprietrary source-available[69] freeware for academic use; commercial license available[70]
Websitewww.rosettacommons.org

Rosetta is the software responsible for performing structure prediction in Rosetta@home. Besides a BOINC cluster, Rosetta can run on a single local computer, or on a local supercomputer. Similar to other bioinformatic programs, there are online public servers offering to run Rosetta from a web interface.[71] The software is freely licensed to the academic community and available to pharmaceutical companies for a fee.[72]

Originally introduced by the Baker laboratory at the University of Washington in 1998 as an ab initio approach to structure prediction, Rosetta has since branched into several development streams and distinct services, providing features such as macromolecular docking and protein design.[67] Many of the graduate students and other researchers involved in Rosetta's initial development have since moved to other universities and research institutions, and subsequently enhanced different parts of the Rosetta project.

The Rosetta platform derives its name from the Rosetta Stone, as it attempts to decipher the structural "meaning" of proteins' amino acid sequences.[73] Development of the Rosetta code is done by Rosetta Commons.[72] Rosetta participates in CASP and CAPRI.

Rosetta was rewritten in C++ to allow easier development than that allowed by its original version, which was written in Fortran. This new version is object-oriented, and was released to Rosetta@Home February 8, 2008.[21][74]

RosettaDesign

edit
 
Superposition of Rosetta-designed model (red) for Top7 onto its X-ray crystal structure (blue, PDB ID: 1QYS)

RosettaDesign, a computing approach to protein design based on Rosetta, began in 2000 with a study in redesigning the folding pathway of Protein G.[75] In 2002 RosettaDesign was used to design Top7, a 93-amino acid long α/β protein that had an overall fold never before recorded in nature. This new conformation was predicted by Rosetta to within 1.2 Å RMSD of the structure determined by X-ray crystallography, representing an unusually accurate structure prediction.[76] Rosetta and RosettaDesign earned widespread recognition by being the first to design and accurately predict the structure of a novel protein of such length, as reflected by the 2002 paper describing the dual approach prompting two positive letters in the journal Science,[77][78] and being cited by more than 240 other scientific articles.[79] The visible product of that research, Top7, was featured as the RCSB PDB's 'Molecule of the Month' in October 2006;[80] a superposition of the respective cores (residues 60–79) of its predicted and X-ray crystal structures are featured in the Rosetta@home logo.[29]

Brian Kuhlman, a former postdoctoral associate in David Baker's lab and now an associate professor at the University of North Carolina, Chapel Hill,[81] offers RosettaDesign as an online service.[82]

RosettaDock

edit

RosettaDock was added to the Rosetta software suite during the first CAPRI experiment in 2002 as the Baker laboratory's algorithm for protein–protein docking prediction.[83] In that experiment, RosettaDock made a high-accuracy prediction for the docking between streptococcal pyogenic exotoxin A and a T cell-receptor β-chain, and a medium accuracy prediction for a complex between porcine α-amylase and a camelid antibody. While the RosettaDock method only made two acceptably accurate predictions out of seven possible, this was enough to rank it seventh out of nineteen prediction methods in the first CAPRI assessment.[83]

Development of RosettaDock diverged into two branches for subsequent CAPRI rounds as Jeffrey Gray, who laid the groundwork for RosettaDock while at the University of Washington, continued working on the method in his new position at Johns Hopkins University. Members of the Baker laboratory further developed RosettaDock in Gray's absence. The two versions differed slightly in side-chain modeling, decoy selection and other areas.[48][84] Despite these differences, both the Baker and Gray methods performed well in the second CAPRI assessment, placing fifth and seventh respectively out of 30 predictor groups.[85] Jeffrey Gray's RosettaDock server is available as a free docking prediction service for non-commercial use.[86]

In October 2006, RosettaDock was integrated into Rosetta@home. The method used a fast, crude docking model phase using only the protein backbone. This was followed by a slow full-atom refinement phase in which the orientation of the two interacting proteins relative to each other, and side-chain interactions at the protein–protein interface, were simultaneously optimized to find the lowest energy conformation.[87] The vastly increased computing power afforded by the Rosetta@home network, combined with revised fold-tree representations for backbone flexibility and loop modeling, made RosettaDock sixth out of 63 prediction groups in the third CAPRI assessment.[6][34]

Robetta

edit

The Robetta (Rosetta Beta) server is an automated protein structure prediction service offered by the Baker laboratory for non-commercial ab initio and comparative modeling.[88] It has participated as an automated prediction server in the biannual CASP experiments since CASP5 in 2002, performing among the best in the automated server prediction category.[89] Robetta has since competed in CASP6 and 7, where it did better than average among both automated server and human predictor groups.[32][90][91] It also participates in the CAMEO3D continuous evaluation. Robetta tasks run on Baker lab servers, Janelia Research Campus machines, and Rosetta@home participant computers.[88]

In modeling protein structure as of CASP6, Robetta first searches for structural homologs using BLAST, PSI-BLAST, and 3D-Jury, then parses the target sequence into its individual domains, or independently folding units of proteins, by matching the sequence to structural families in the Pfam database. Domains with structural homologs then follow a "template-based model" (i.e., homology modeling) protocol. Here, the Baker laboratory's in-house alignment program, K*sync, produces a group of sequence homologs, and each of these is modeled by the Rosetta de novo method to produce a decoy (possible structure). The final structure prediction is selected by taking the lowest energy model as determined by a low-resolution Rosetta energy function. For domains that have no detected structural homologs, a de novo protocol is followed in which the lowest energy model from a set of generated decoys is selected as the final prediction. These domain predictions are then connected together to investigate inter-domain, tertiary-level interactions within the protein. Finally, side-chain contributions are modeled using a protocol for Monte Carlo conformational search.[92]

In CASP8, Robetta was augmented to use Rosetta's high resolution all-atom refinement method,[93] the absence of which was cited as the main cause for Robetta being less accurate than the Rosetta@home network in CASP7.[33] In CASP11, a way to predict the protein contact map by co-evolution of residues in related proteins called GREMLIN was added, allowing for more de novo fold successes.[94]

Other Rosetta servers

edit

Rosetta is available as an online service from a number of other public servers. ROSIE offers a variety of functions from RNA structure prediction and design to ligand docking and antibody modeling.[95]

Foldit

edit
See also: Foldit

On May 9, 2008, after Rosetta@home users suggested an interactive version of the volunteer computing program, the Baker lab publicly released Foldit, an online protein structure prediction game based on the Rosetta platform.[96] As of September 25, 2008, Foldit had over 59,000 registered users.[97] The game gives users a set of controls (for example, shake, wiggle, rebuild) to manipulate the backbone and amino acid side chains of the target protein into more energetically favorable conformations. Users can work on solutions individually as soloists or collectively as evolvers, accruing points under either category as they improve their structure predictions.[98]

Foldit can work as a GUI frontend to Rosetta under a tailored "professional mode".[71]

RoseTTAFold

edit

RoseTTAFold, which is inspired by AlphaFold, uses a neural network to predict the distance and orientation between residues. These predictions guide Rosetta software in producing a structure. RoseTTAFold is open source under the MIT license.[99]

Non-Baker lab branches

edit

The Jianyi Yang lab in China offers a modified version of Rosetta termed tr-RosettaX2 (transform-restrained Rosetta).[100] It uses a deep learning-based contact prediction method different from RoseTTAFold to guide the usual Rosetta folding algorithm. trRosetta predates RoseTTAFold.[101]

Comparison to similar volunteer computing projects

edit

There are several volunteer computed projects which have study areas similar to those of Rosetta@home, but differ in their research approach:

Folding@home

edit

Of all the major volunteer computing projects involved in protein research, Folding@home is the only one not using the BOINC platform.[102][103][104] Both Rosetta@home and Folding@home study protein misfolding diseases such as Alzheimer's disease, but Folding@home does so much more exclusively.[105][106] Folding@home almost exclusively uses all-atom molecular dynamics models to understand how and why proteins fold (or potentially misfold, and subsequently aggregate to cause diseases).[107][108] In other words, Folding@home's strength is modeling the process of protein folding, while Rosetta@home's strength is computing protein design and predicting protein structure and docking.

Some of Rosetta@home's results are used as the basis for some Folding@home projects. Rosetta provides the most likely structure, but it is not definite if that is the form the molecule takes or whether or not it is viable. Folding@home can then be used to verify Rosetta@home's results, and can provide added atomic-level information, and details of how the molecule changes shape.[108][109]

The two projects also differ significantly in their computing power and host diversity. Averaging about 6,650 teraFLOPS from a host base of central processing units (CPUs), graphics processing units (GPUs), and (formerly) PS3s,[110] Folding@home has nearly 108 times more computing power than Rosetta@home.[111]

World Community Grid

edit

Both Phase I and Phase II of the Human Proteome Folding Project (HPF), a subproject of World Community Grid, have used the Rosetta program to make structural and functional annotations of various genomes.[112][113] Although he now uses it to create databases for biologists, Richard Bonneau, head scientist of the Human Proteome Folding Project, was active in the original development of Rosetta at David Baker's laboratory while obtaining his PhD.[114] More information on the relationship between the HPF1, HPF2 and Rosetta@home can be found on Richard Bonneau's website.[115]

Predictor@home

edit

Like Rosetta@home, Predictor@home specialized in protein structure prediction.[116] While Rosetta@home uses the Rosetta program for its structure prediction, Predictor@home used the dTASSER methodology.[117] In 2009, Predictor@home shut down.

Other protein related volunteer computing projects on BOINC include QMC@home, Docking@home, POEM@home, SIMAP, and TANPAKU. RALPH@home, the Rosetta@home alpha project which tests new application versions, work units, and updates before they move on to Rosetta@home, runs on BOINC also.[118]

Volunteer contributions

edit

Rosetta@home depends on computing power donated by individual project members for its research. As of March 28, 2020, about 53,000 users from 150 countries were active members of Rosetta@home, together contributing idle processor time from about 54,800 computers for a combined average performance of over 1.7 PetaFLOPS.[111][119]

 
Bar chart showing cumulative credit per day for Rosetta@home over a 60-day period, indicating its computing power during the CASP8 experiment

Users are granted BOINC credits as a measure of their contribution. The credit granted for each workunit is the number of decoys produced for that workunit multiplied by the average claimed credit for the decoys submitted by all computer hosts for that workunit. This custom system was designed to address significant differences between credit granted to users with the standard BOINC client and an optimized BOINC client, and credit differences between users running Rosetta@home on Windows and Linux operating systems.[120] The amount of credit granted per second of CPU work is lower for Rosetta@home than most other BOINC projects.[121] Rosetta@home is thirteenth out of over 40 BOINC projects in terms of total credit.[122]

Rosetta@home users who predict protein structures submitted for the CASP experiment are acknowledged in scientific publications regarding their results.[33] Users who predict the lowest energy structure for a given workunit are featured on the Rosetta@home homepage as Predictor of the Day, along with any team of which they are a member.[123] A User of the Day is chosen randomly each day to be on the homepage also, from among users who have made a Rosetta@home profile.[124]

References

edit
  1. ^ "Rosetta@home License Agreement". Boinc.bakerlab.org. Archived from the original on June 12, 2020. Retrieved October 27, 2024.
  2. ^ "Rosetta@home". Archived from the original on August 7, 2024. Retrieved September 23, 2024.
  3. ^ "Rosetta@Home – Detailed stats | BOINCstats/BAM!". Archived from the original on February 11, 2019. Retrieved October 20, 2018.
  4. ^ "Rosetta@home". Archived from the original on March 14, 2016. Retrieved March 24, 2020.
  5. ^ "What is Rosetta@home?". Rosetta@home forums. University of Washington. Archived from the original on September 13, 2008. Retrieved September 7, 2008.
  6. ^ a b Lensink MF, Méndez R, Wodak SJ (December 2007). "Docking and scoring protein complexes: CAPRI 3rd Edition". Proteins. 69 (4): 704–18. doi:10.1002/prot.21804. PMID 17918726. S2CID 25383642.
  7. ^ "Rosetta@home - Server Status "TeraFLOPS estimate"". Rosetta@home. March 28, 2020. Archived from the original on January 3, 2016. Retrieved March 28, 2020.
  8. ^ "Rosetta@home Rallies a Legion of Computers Against the Coronavirus". HPCWire. March 24, 2020. Archived from the original on April 9, 2020. Retrieved March 25, 2020.
  9. ^ a b c "The COVID-19 projects on our platform are headed into human clinical trials! Our amazing online volunteers have played a role in the development of a promising new vaccine as well as candidate antiviral treatments". Twitter. June 25, 2021. Archived from the original on June 26, 2021. Retrieved June 26, 2021.
  10. ^ a b c Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, et al. (October 2020). "De novo design of picomolar SARS-CoV-2 miniprotein inhibitors". Science. 370 (6515): 426–431. Bibcode:2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
  11. ^ "Coronavirus update from David Baker. Thank you all for your contributions!". Rosetta@home. September 21, 2020. Archived from the original on October 30, 2020. Retrieved September 23, 2020.
  12. ^ a b c "IPD Annual Report 2021" (PDF). Institute for Protein Design. July 14, 2021. Archived (PDF) from the original on August 18, 2021. Retrieved August 18, 2021.
  13. ^ a b "ANZCTR - Registration". anzctr.org.au. Archived from the original on October 30, 2021. Retrieved July 9, 2021.
  14. ^ a b "S. Korea approves Phase III trial of SK Bioscience's COVID-19 vaccine". Reuters. August 10, 2021. Archived from the original on August 18, 2021. Retrieved August 18, 2021.
  15. ^ a b Institute of Protein Design (August 10, 2021). "Archived copy". Twitter. Archived from the original on August 18, 2021. Retrieved August 18, 2021.{{cite web}}: CS1 maint: archived copy as title (link)
  16. ^ a b Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). "De novo design of potent and selective mimics of IL-2 and IL-15". Nature. 565 (7738): 186–191. Bibcode:2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
  17. ^ a b "Neoleukin Therapeutics Announces Initiation of Phase 1 NL-201 Trial | Neoleukin Therapeutics, Inc". investor.neoleukin.com. Archived from the original on June 24, 2021. Retrieved June 22, 2021.
  18. ^ a b "Another publication in Nature describing the first de novo designed proteins with anti-cancer activity". Rosetta@home. January 14, 2020. Archived from the original on October 19, 2020. Retrieved September 19, 2020.
  19. ^ a b "Download BOINC client software". BOINC. University of California. 2008. Archived from the original on December 7, 2008. Retrieved December 1, 2008.
  20. ^ "Rosetta@home: Recommended System Requirements". Rosetta@home. University of Washington. 2008. Archived from the original on September 25, 2008. Retrieved October 7, 2008.
  21. ^ a b "Rosetta@home: News archive". Rosetta@home. University of Washington. 2016. Archived from the original on June 16, 2016. Retrieved July 20, 2016.
  22. ^ "Rosetta@home: FAQ (work in progress) (message 10910)". Rosetta@home forums. University of Washington. 2006. Archived from the original on February 26, 2009. Retrieved October 7, 2008.
  23. ^ Kim DE (2005). "Rosetta@home: Random Seed (message 3155)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved October 7, 2008.
  24. ^ "Rosetta@home: Quick guide to Rosetta and its graphics". Rosetta@home. University of Washington. 2007. Archived from the original on September 24, 2008. Retrieved October 7, 2008.
  25. ^ Bourne PE, Helge W, eds. (2003). Structural Bioinformatics. Hoboken, NJ: Wiley-Liss. ISBN 978-0-471-20199-1. OCLC 50199108.
  26. ^ "Yearly Growth of Protein Structures". RCSB Protein Data Bank. 2021. Archived from the original on May 1, 2021. Retrieved May 1, 2021.
  27. ^ Baker D (2008). "Rosetta@home: David Baker's Rosetta@home journal (message 55893)". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved October 7, 2008.
  28. ^ Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A. Patricia; Donadi, Ramesh S.; Bologna, Cristian G.; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I.; Overington, John P. (December 2, 2016). "A comprehensive map of molecular drug targets". Nature Reviews Drug Discovery. 16 (1): 19–34. doi:10.1038/nrd.2016.230. PMC 6314433. PMID 27910877.
  29. ^ a b "Rosetta@home: Research Overview". Rosetta@home. University of Washington. 2007. Archived from the original on September 25, 2008. Retrieved October 7, 2008.
  30. ^ Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007). "Assessment of CASP7 predictions for template-based modeling targets". Proteins. 69 (Suppl 8): 38–56. doi:10.1002/prot.21753. PMID 17894352. S2CID 31575350.
  31. ^ Read RJ, Chavali G (2007). "Assessment of CASP7 predictions in the high accuracy template-based modeling category". Proteins. 69 (Suppl 8): 27–37. doi:10.1002/prot.21662. PMID 17894351. S2CID 33172629.
  32. ^ a b Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007). "Assessment of CASP7 structure predictions for template free targets". Proteins. 69 (Suppl 8): 57–67. doi:10.1002/prot.21771. PMID 17894330. S2CID 38430899.
  33. ^ a b c Das R, Qian B, Raman S, et al. (2007). "Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home". Proteins. 69 (Suppl 8): 118–28. doi:10.1002/prot.21636. PMID 17894356. S2CID 17470364.
  34. ^ a b Wang C, Schueler-Furman O, Andre I, et al. (December 2007). "RosettaDock in CAPRI rounds 6–12". Proteins. 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979. S2CID 9028237. A large amount of docking computation for the pre-dictions of target 27 and 28 was carried out on Rosetta@Home (www.boinc.bakerlab.org), a distributed comput-ing project running Rosetta software on personal com-puters of volunteers from all over the world using the Berkeley Open Infrastructure for Network Computing (BOINC) technology (www.boinc.berkeley.edu).
  35. ^ a b c Jiang L, Althoff EA, Clemente FR, et al. (March 2008). "De novo computational design of retro-aldol enzymes". Science. 319 (5868): 1387–91. Bibcode:2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
  36. ^ Hayden EC (February 13, 2008). "Protein prize up for grabs after retraction". Nature. doi:10.1038/news.2008.569.
  37. ^ https://www.nobelprize.org/uploads/2024/10/advanced-chemistryprize2024.pdf
  38. ^ a b "Disease Related Research". Rosetta@home. University of Washington. 2008. Archived from the original on September 23, 2008. Retrieved October 8, 2008.
  39. ^ Baker D (2008). "Rosetta@home: David Baker's Rosetta@home journal". Rosetta@home forums. University of Washington. Archived from the original on September 25, 2008. Retrieved September 7, 2008.
  40. ^ "Rosetta@home Research Updates". Boinc.bakerlab.org. Archived from the original on April 19, 2014. Retrieved April 18, 2014.
  41. ^ "News archive". Rosetta@home. Archived from the original on May 10, 2019. Retrieved May 10, 2019.
  42. ^ Kuhlman B, Baker D (September 2000). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences of the United States of America. 97 (19): 10383–88. Bibcode:2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
  43. ^ Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). "The 3D profile method for identifying fibril-forming segments of proteins". Proceedings of the National Academy of Sciences of the United States of America. 103 (11): 4074–78. Bibcode:2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
  44. ^ Bradley P. "Rosetta@home forum: Amyloid fibril structure prediction". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
  45. ^ Baker D. "Rosetta@home forum: Publications on R@H's Alzheimer's work? (message 54681)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved October 8, 2008.
  46. ^ Wang C, Schueler-Furman O, Baker D (May 2005). "Improved side-chain modeling for protein–protein docking". Protein Science. 14 (5): 1328–39. doi:10.1110/ps.041222905. PMC 2253276. PMID 15802647.
  47. ^ Gray JJ, Moughon S, Wang C, et al. (August 2003). "Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations". Journal of Molecular Biology. 331 (1): 281–99. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852.
  48. ^ a b Schueler-Furman O, Wang C, Baker D (August 2005). "Progress in protein–protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility". Proteins. 60 (2): 187–94. doi:10.1002/prot.20556. PMID 15981249. S2CID 17672050.
  49. ^ Lacy DB, Lin HC, Melnyk RA, et al. (November 2005). "A model of anthrax toxin lethal factor bound to protective antigen". Proceedings of the National Academy of Sciences of the United States of America. 102 (45): 16409–14. Bibcode:2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
  50. ^ Albrecht MT, Li H, Williamson ED, et al. (November 2007). "Human monoclonal antibodies against anthrax lethal factor and protective antigen act independently to protect against Bacillus anthracis infection and enhance endogenous immunity to anthrax". Infection and Immunity. 75 (11): 5425–33. doi:10.1128/IAI.00261-07. PMC 2168292. PMID 17646360.
  51. ^ Sprague ER, Wang C, Baker D, Bjorkman PJ (June 2006). "Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging". PLOS Biology. 4 (6): e148. doi:10.1371/journal.pbio.0040148. PMC 1450327. PMID 16646632.
  52. ^ Paulson, Tom (July 19, 2006). "Gates Foundation awards $287 million for HIV vaccine research". Seattle Post-Intelligencer. Archived from the original on September 5, 2022. Retrieved September 7, 2008.
  53. ^ Liu Y, et al. (2007). "Development of IgG1 b12 scaffolds and HIV-1 env-based outer domain immunogens capable of eliciting and detecting IgG1 b12-like antibodies" (PDF). Global HIV Vaccine Enterprise. Archived from the original (PDF) on February 25, 2009. Retrieved September 28, 2008.
  54. ^ Baker D. "David Baker's Rosetta@home journal archives (message 40756)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
  55. ^ "Homing Endonuclease Genes: New Tools for Mosquito Population Engineering and Control". Grand Challenges in Global Health. Archived from the original on July 6, 2008. Retrieved September 7, 2008.
  56. ^ Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007). "Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos". Nucleic Acids Research. 35 (17): 5922–33. doi:10.1093/nar/gkm632. PMC 2034484. PMID 17726053.
  57. ^ Ashworth J, Havranek JJ, Duarte CM, et al. (June 2006). "Computational redesign of endonuclease DNA binding and cleavage specificity". Nature. 441 (7093): 656–59. Bibcode:2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
  58. ^ "Rosetta's role in fighting coronavirus – Institute for Protein Design". February 21, 2020. Archived from the original on December 24, 2021. Retrieved March 6, 2020.
  59. ^ "Coronavirus Research Update". Rosetta@home Official Twitter. June 26, 2020. Archived from the original on June 26, 2020. Retrieved June 27, 2020.
  60. ^ Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, et al. (July 2021). "Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease". Cell Host & Microbe. 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
  61. ^ Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, et al. (July 2021). "Multivalent designed proteins protect against SARS-CoV-2 variants of concern". bioRxiv: 2021.07.07.451375. doi:10.1101/2021.07.07.451375. PMC 8282097. PMID 34268509.
  62. ^ "Big news out of @UWproteindesign: a new candidate treatment for #COVID19! More lab testing still needed. Thanks to all the volunteers who helped crunch data for this project!!". Rosetta@home Twitter. September 9, 2020. Archived from the original on September 9, 2020. Retrieved September 19, 2020.
  63. ^ "De novo minibinders target SARS-CoV-2 Spike protein". Baker Lab. September 9, 2020. Archived from the original on September 30, 2020. Retrieved September 19, 2020.
  64. ^ Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, et al. (November 2020). "Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2". Cell. 183 (5): 1367–1382.e17. doi:10.1016/j.cell.2020.10.043. PMC 7604136. PMID 33160446.
  65. ^ Hutson M (September 18, 2020). "Scientists Advance on One of Technology's Holy Grails". The New Yorker. Archived from the original on September 18, 2020. Retrieved September 19, 2020.
  66. ^ "Neoleukin Therapeutics Announces Submission of Investigational New Drug Application for NL-201 De Novo Protein Immunotherapy Candidate for Cancer". Neoleukin Therapeutics. December 10, 2020. Archived from the original on December 10, 2020. Retrieved December 10, 2020.
  67. ^ a b Simons KT, Bonneau R, Ruczinski I, Baker D (1999). "Ab initio protein structure prediction of CASP III targets using Rosetta". Proteins. Suppl 3 (S3): 171–76. doi:10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z. PMID 10526365. S2CID 5774447.
  68. ^ "Release Notes". Rosetta Commons. Retrieved August 21, 2023.
  69. ^ "Getting started". www.rosettacommons.org. We don't distribute executables/binaries for most purposes, we distribute source code.
  70. ^ "Rosetta: a molecular modeling software package". UW CoMotion – Collaborative Innovation Hub. Archived from the original on June 12, 2020. Retrieved June 12, 2020.
  71. ^ a b "Ways to Use". RosettaCommons. July 14, 2023.
  72. ^ a b "Rosetta Commons". RosettaCommons.org. 2008. Archived from the original on September 15, 2008. Retrieved October 7, 2008.
  73. ^ "Interview with David Baker". Team Picard Distributed Computing. 2006. Archived from the original on February 18, 2009. Retrieved December 23, 2008.
  74. ^ Kim DE (2008). "Rosetta@home: Problems with minirosetta version 1.+ (Message 51199)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
  75. ^ Nauli S, Kuhlman B, Baker D (July 2001). "Computer-based redesign of a protein folding pathway". Nature Structural Biology. 8 (7): 602–05. doi:10.1038/89638. PMID 11427890. S2CID 18542707.
  76. ^ Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (November 2003). "Design of a novel globular protein fold with atomic-level accuracy". Science. 302 (5649): 1364–68. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033. S2CID 1939390.
  77. ^ Jones DT (November 2003). "Structural biology. Learning to speak the language of proteins". Science. 302 (5649): 1347–48. doi:10.1126/science.1092492. PMID 14631028. S2CID 83109899.
  78. ^ von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L (June 2004). "Predicting protein structures accurately". Science. 304 (5677): 1597–99, author reply 1597–99. doi:10.1126/science.304.5677.1597b. PMID 15192202. S2CID 29787060.
  79. ^ "Articles citing: Kuhlman et al. (2003) 'Design of a novel globular protein fold with atomic-level accuracy'". ISI Web of Science. Retrieved July 10, 2008.
  80. ^ "October 2005 molecule of the month: Designer proteins". RCSB Protein Data Bank. Archived from the original on September 28, 2008. Retrieved September 7, 2008.
  81. ^ "Kuhlman laboratory homepage". Kuhlman Laboratory. University of North Carolina. Archived from the original on October 10, 2008. Retrieved September 7, 2008.
  82. ^ "RosettaDesign web server". Kuhlman Laboratory. University of North Carolina. Archived from the original on September 13, 2008. Retrieved September 7, 2008.
  83. ^ a b Gray JJ, Moughon SE, Kortemme T, et al. (July 2003). "Protein–protein docking predictions for the CAPRI experiment". Proteins. 52 (1): 118–22. CiteSeerX 10.1.1.80.9354. doi:10.1002/prot.10384. PMID 12784377. S2CID 1186127.
  84. ^ Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005). "CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock". Proteins. 60 (2): 181–86. CiteSeerX 10.1.1.521.9981. doi:10.1002/prot.20555. PMID 15981262. S2CID 21137936. Archived from the original on June 30, 2012.
  85. ^ Méndez R, Leplae R, Lensink MF, Wodak SJ (2005). "Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures". Proteins. 60 (2): 150–69. doi:10.1002/prot.20551. PMID 15981261. S2CID 24626361. Archived from the original on June 30, 2012.
  86. ^ "RosettaDock server". Rosetta Commons. Archived from the original on March 27, 2020. Retrieved March 28, 2020.
  87. ^ "Protein–protein docking at Rosetta@home". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 7, 2008.
  88. ^ a b "Robetta". robetta.bakerlab.org. Computing resources are provided by the Baker lab, HHMI's Janelia Research Campus, and by volunteers from the distributed computing project Rosetta@home. You can help this service by joining Rosetta@home.
  89. ^ Aloy P, Stark A, Hadley C, Russell RB (2003). "Predictions without templates: new folds, secondary structure, and contacts in CASP5". Proteins. 53 (Suppl 6): 436–56. doi:10.1002/prot.10546. PMID 14579333. S2CID 22274928.
  90. ^ Tress M, Ezkurdia I, Graña O, López G, Valencia A (2005). "Assessment of predictions submitted for the CASP6 comparative modeling category". Proteins. 61 (Suppl 7): 27–45. doi:10.1002/prot.20720. PMID 16187345. S2CID 24617067.
  91. ^ Battey JN, Kopp J, Bordoli L, Read RJ, Clarke ND, Schwede T (2007). "Automated server predictions in CASP7". Proteins. 69 (Suppl 8): 68–82. doi:10.1002/prot.21761. PMID 17894354. S2CID 29879391.
  92. ^ Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D (2005). "Prediction of CASP6 structures using automated Robetta protocols". Proteins. 61 (Suppl 7): 157–66. doi:10.1002/prot.20733. PMID 16187358. S2CID 8122486.
  93. ^ Baker D. "David Baker's Rosetta@home journal, message 52902". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 7, 2008.
  94. ^ Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D (September 2016). "Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta". Proteins. 84 (Suppl 1): 67–75. doi:10.1002/prot.24974. PMC 5490371. PMID 26677056.
  95. ^ "Servers". RosettaCommons. July 14, 2023.
  96. ^ Baker D. "David Baker's Rosetta@home journal (message 52963)". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 16, 2008.
  97. ^ "Foldit forums: How many users does Foldit have? Etc. (message 2)". University of Washington. Archived from the original on September 22, 2008. Retrieved September 27, 2008.
  98. ^ "Foldit: Frequently Asked Questions". fold.it. University of Washington. Archived from the original on September 14, 2008. Retrieved September 19, 2008.
  99. ^ Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N.; Schaeffer, R. Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R.; DeGiovanni, Andy; Pereira, Jose H.; Rodrigues, Andria V.; van Dijk, Alberdina A.; Ebrecht, Ana C.; Opperman, Diederik J.; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K.; Dalwadi, Udit; Yip, Calvin K.; Burke, John E.; Garcia, K. Christopher; Grishin, Nick V.; Adams, Paul D.; Read, Randy J.; Baker, David (August 20, 2021). "Accurate prediction of protein structures and interactions using a three-track neural network". Science. 373 (6557): 871–876. Bibcode:2021Sci...373..871B. doi:10.1126/science.abj8754. PMC 7612213. PMID 34282049.
  100. ^ Peng, Z; Wang, W; Han, R; Zhang, F; Yang, J (December 2022). "Protein structure prediction in the deep learning era". Current Opinion in Structural Biology. 77: 102495. doi:10.1016/j.sbi.2022.102495. PMID 36371845. S2CID 253470306.
  101. ^ Du, Zongyang; Su, Hong; Wang, Wenkai; Ye, Lisha; Wei, Hong; Peng, Zhenling; Anishchenko, Ivan; Baker, David; Yang, Jianyi (December 2021). "The trRosetta server for fast and accurate protein structure prediction". Nature Protocols. 16 (12): 5634–5651. doi:10.1038/s41596-021-00628-9. PMID 34759384. S2CID 243987300.
  102. ^ "Project list – BOINC". University of California. Archived from the original on September 8, 2008. Retrieved September 8, 2008.
  103. ^ Pande Group (2010). "High Performance FAQ". Stanford University. Archived from the original (FAQ) on August 19, 2012. Retrieved September 19, 2011.
  104. ^ 7im (April 2, 2010). "Re: Answers to: Reasons for not using F@H". Archived from the original on August 24, 2021. Retrieved September 19, 2011.{{cite web}}: CS1 maint: numeric names: authors list (link)
  105. ^ Vijay Pande (August 5, 2011). "Results page updated – new key result published in our work in Alzheimer's Disease". Archived from the original on September 15, 2011. Retrieved September 19, 2011.
  106. ^ Pande Group. "Folding@home Diseases Studied FAQ". Stanford University. Archived from the original (FAQ) on October 11, 2007. Retrieved September 12, 2011.
  107. ^ Vijay Pande (September 26, 2007). "How FAH works: Molecular dynamics". Archived from the original on September 26, 2011. Retrieved September 10, 2011.
  108. ^ a b tjlane (June 9, 2011). "Re: Course grained Protein folding in under 10 minutes". Archived from the original on November 11, 2012. Retrieved September 19, 2011.
  109. ^ jmn (July 29, 2011). "Rosetta@home and Folding@home: additional projects". Archived from the original on September 23, 2011. Retrieved September 19, 2011.
  110. ^ Pande Group. "Client Statistics by OS". Stanford University. Archived from the original on May 13, 2013. Retrieved October 18, 2011.
  111. ^ a b "Rosetta@home: Credit overview". boincstats.com. Archived from the original on April 21, 2020. Retrieved March 28, 2020.
  112. ^ Malmström L, Riffle M, Strauss CE, et al. (April 2007). "Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology". PLOS Biology. 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
  113. ^ Bonneau R (2006). "World Community Grid Message Board Posts: HPF -> HPF2 transition". Bonneau Lab, New York University. Archived from the original on August 29, 2008. Retrieved September 7, 2008.
  114. ^ "List of Richard Bonneau's publications". Bonneau Lab, New York University. Archived from the original on July 7, 2008. Retrieved September 7, 2008.
  115. ^ Bonneau R. "World Community Grid Message Board Posts". Bonneau Lab, New York University. Archived from the original on July 4, 2008. Retrieved September 7, 2008.
  116. ^ "Predictor@home: Developing new application areas for P@H". The Brooks Research Group. Retrieved September 7, 2008.[dead link]
  117. ^ Carrillo-Tripp M (2007). "dTASSER". The Scripps Research Institute. Archived from the original on July 6, 2007. Retrieved September 7, 2008.
  118. ^ "RALPH@home website". RALPH@home forums. University of Washington. Archived from the original on January 13, 2016. Retrieved September 7, 2008.
  119. ^ "Rosetta@home". Archived from the original on January 3, 2016. Retrieved March 19, 2020.
  120. ^ "Rosetta@home: The new credit system explained". Rosetta@home forums. University of Washington. 2006. Archived from the original on February 2, 2009. Retrieved October 8, 2008.
  121. ^ "BOINCstats: Project Credit Comparison". boincstats.com. 2008. Archived from the original on September 13, 2008. Retrieved October 8, 2008.
  122. ^ "Credit divided over projects". boincstats.com. Archived from the original on February 20, 2015. Retrieved February 19, 2015.
  123. ^ "Rosetta@home: Predictor of the day archive". Rosetta@home. University of Washington. 2008. Archived from the original on September 24, 2008. Retrieved October 8, 2008.
  124. ^ "Rosetta@home: Protein Folding, Design, and Docking". Rosetta@home. University of Washington. 2008. Archived from the original on February 28, 2011. Retrieved October 8, 2008.
edit

Online Rosetta services

 
Wikimedia Commons has media related to Rosetta@home.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Rosetta@home&oldid=1253640106"
pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy