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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Vijay S. Pande, Ian Baker, Jarrod Chapman, Sidney P. Elmer, Siraj Khaliq, Stefan M. Larson, Young Min Rhee, Michael R. Shirts, Christopher D. Snow, Eric J. Sorin, Bojan Zagrovic
2002 Biopolymers  
Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds
more » ... atomistic molecular dynamics. This has allowed us to directly Correspondence to: Vijay S. Pande; 91 simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide ␣-helices, a ␤-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.
doi:10.1002/bip.10219 pmid:12579582 fatcat:ydtvvauibrg2jgjcb5hc73v3le

Projecting Marine Mammal Distribution in a Changing Climate

Gregory K. Silber, Matthew D. Lettrich, Peter O. Thomas, Jason D. Baker, Mark Baumgartner, Elizabeth A. Becker, Peter Boveng, Dorothy M. Dick, Jerome Fiechter, Jaume Forcada, Karin A. Forney, Roger B. Griffis (+13 others)
2017 Frontiers in Marine Science  
., dynamic shoreline evolution) for forecasting its distribution (Baker et al., 2006) .  ...  Copyright © 2017 Silber, Lettrich, Thomas, Baker, Baumgartner, Becker, Boveng, Dick, Fiechter, Forcada, Forney, Griffis, Hare, Hobday, Howell, Laidre, Mantua, Quakenbush, Santora, Stafford, Spencer, Stock  ... 
doi:10.3389/fmars.2017.00413 fatcat:lkpbzu7fkvd45jfldmolfrd7iu

Open Targets Platform: supporting systematic drug–target identification and prioritisation

David Ochoa, Andrew Hercules, Miguel Carmona, Daniel Suveges, Asier Gonzalez-Uriarte, Cinzia Malangone, Alfredo Miranda, Luca Fumis, Denise Carvalho-Silva, Michaela Spitzer, Jarrod Baker, Javier Ferrer (+20 others)
2020 Nucleic Acids Research  
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target–disease relationships from 20 different data sources. In addition, we have
more » ... rated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.
doi:10.1093/nar/gkaa1027 pmid:33196847 fatcat:3qrm5q5turgulbvyj2kj6oy5c4

Autonomous driving in urban environments: Boss and the Urban Challenge

Chris Urmson, Joshua Anhalt, Drew Bagnell, Christopher Baker, Robert Bittner, M. N. Clark, John Dolan, Dave Duggins, Tugrul Galatali, Chris Geyer, Michele Gittleman, Sam Harbaugh (+30 others)
2008 Journal of Field Robotics  
moving object hypotheses that are not fully on a road can be ignored for distance-keeping purposes, as they likely represent vehicles parked at the side of the road or other static obstacles (Darms, Baker  ... 
doi:10.1002/rob.20255 fatcat:ivab3r3m6bdfvhdlwnd5mdrzne

Autonomous Driving in Urban Environments: Boss and the Urban Challenge [chapter]

Chris Urmson, Joshua Anhalt, Drew Bagnell, Christopher Baker, Robert Bittner, M. N. Clark, John Dolan, Dave Duggins, Tugrul Galatali, Chris Geyer, Michele Gittleman, Sam Harbaugh (+30 others)
2009 Springer Tracts in Advanced Robotics  
moving object hypotheses that are not fully on a road can be ignored for distance-keeping purposes, as they likely represent vehicles parked at the side of the road or other static obstacles (Darms, Baker  ... 
doi:10.1007/978-3-642-03991-1_1 fatcat:l6hb3cyxcraijctglkr2mobcxu

PACT: Parents and children together in phonological therapy

Caroline Bowen, L. Cupples
2006 Advances in Speech Language Pathology  
Difficulties in applying the PACT approach with Jarrod are noted, principally that PACT is most suited to the three to six year age-group. Alternative intervention approaches are suggested.  ...  assessment using parent-observed screening, independent and relational analyses, treatment planning and scheduling, and target selection and goal-setting are presented and discussed in the context of Jarrod  ...  Acknowledgements Thanks are extended to Jarrod for his patient, concentrated effort and good humour as the key figure in this project, and to A.  ... 
doi:10.1080/14417040600826980 fatcat:fqqob2yvvfhobpssocyl7jw4wm

Intervention for a child with persisting speech and literacydifficulties: A psycholinguistic approach

Joy Stackhouse, Michelle Pascoe, Hilary Gardner
2006 Advances in Speech Language Pathology  
A psycholinguistic approach can be helpful for children like Jarrod as it tackles speech and literacy simultaneously and has inbuilt assessments, monitoring and evaluation.  ...  This paper illustrates a psycholinguistic approach to investigating children's speech and literacy difficulties by describing a "three-way" intervention plan for Jarrod, a 7 year old boy with unintelligible  ...  difficulties are occurring; only a psycholinguistic investigation of his speech input, output and representations will reveal if his difficulties are specific to the output level or more pervasive (Baker  ... 
doi:10.1080/14417040600861029 fatcat:5priq2rk2vd2fm32icv3urptwa

A systematic perspective for assessment and intervention: A case study

A. Lynn Williams
2006 Advances in Speech Language Pathology  
A systemic perspective was employed in completing a phonological analysis and developing an intervention plan for Jarrod, a 7;0 year old child who exhibited a severe speech sound disorder characterized  ...  A couple of studies have compared the differences in target selection resulting from divergent assessments of the sound system of one child (Baker & Bernhardt, 2004; Dyer-Mistone, Guello, & Williams,  ...  Open boxes represent consonants that are part of the English inventory, but were never produced by Jarrod.  ... 
doi:10.1080/14417040600823292 fatcat:o4f77zhjsrbvviwmvlqb2pttui

Improving Collaboration for Effective Violence Surveillance and Health Promotion

Daniel J. Schober, Megha Ramaswamy, Won Sup Choi, Stephen B. Fawcett, Jarrod Hindman, Jeremy M. Martinez
2011 Journal of Public Health Management and Practice  
Fawcett, PhD; Jarrod Hindman, MS; Jeremy M.  ...  Uses of behavioral ri lata 1993 1997 Figgs LW, Baker EA, Dugbatey K, Stan Brownson RC.  ... 
doi:10.1097/phh.0b013e3181f5424a pmid:21297414 fatcat:ksia2qf7qbcglezobedhhetmdi

Page 1 of Chemist Vol. 69, Issue 11 [page]

1992 Chemist  
Ronneberg Jarrod Smith Mark Wall Kristen L. Anderson Joseph Barbosa Dorian Calderon Adelaide J. Castellano Alfredo Cardona Mary P. Carson Louis Coless Susan E. Craig Yvonne M.  ...  State University College of Saint Elizabeth Trenton State College Princeton University Trenton State College KCIC Mid-America Nazarene Coll Benedictine College University of Kansas Rockhurst College Baker  ... 

Unsettling Reflections

Melissa Munn, Kevin Walby
1969 Journal of Prisoners on Prisons  
For example, Jarrod Shook demands accountability in how prisoner security classifi cation and pay for labour is determined in Canada's federal prisons.  ...  Zaineb Mohammed refl ects on the various projects of the Ella Baker Centre for Human Rights, while Madeleine Spain discusses the work of Justice Action in Prisons.  ... 
doi:10.18192/jpp.v24i1.5051 fatcat:oxiehdmbjnhohh6sy5oaoqn6ji

Page 1017 of The Journal of Ecology Vol. 92, Issue 6 [page]

2004 The Journal of Ecology  
Acknowledgements We are grateful to Veijo Jormalainen, an anonymous reviewer and Jarrod Stehbens for comments that improved the manuscript.  ...  Baker), pp. 325-353. CRC Press, Boca Raton, Florida. Cronin, G. & Hay, M.E. (1996a) Induction of seaweed chemical defenses by amphipod grazing. Ecology, 77, 2287-2301.  ... 

A Non-Systematic Review of Evidence-Based Practice within Speech Pathology in Australia

Sharynne McLeod
2008 South African Journal of Communication Disorders  
For example, M cLeod and Baker (2004) examined Australian speech pathologists' clinical practice for children with speech impairment and Watts Pappas, M cLeod, McAllister and M cKinnon (2008) studied  ...  The special issue SHARYNNE M CLEO D was accompanied by online video files to enable clinicians to develop their clinical expertise by reflecting on their clinical decision making for Jarrod.  ... 
doi:10.4102/sajcd.v55i1.765 fatcat:hp25on5ocvbvhawslcf6teuzne

Page 35 of Guernsey Breeders' Journal Vol. 161, Issue 3 [page]

1992 Guernsey Breeders' Journal  
Buffington, Millersburg, PA Cara Burllngham, Malone, W1 Charles Kevin Cornett, Manchester, KY Jarrod Brent Cornett, Manchester, KY Cory Craig, Bunker Hill, IN Joel A.  ...  19720M 841F 688P FLAMBEAU MANOR DARLA 3-04 305D-2X 18480M 728F 663P FLAMBEAU MANOR ELOISE VANDEN HEUVEL DAVID 3-02 305D-2X 17120M 741F 629P SPRING FLO ANDYS BERRY 7-03 305D-2X 21720M 1072F 700P SPRING FLO BAKERS  ... 

DOE Computational Science Graduate Fellowship Research Showcase

Jaydeep Bardhan, Mary Ann Leung, Eileen Martin, Amanda Randles
2021 Computing in science & engineering (Print)  
Rounding out the special issue is "From Molecules to Quantum Computers, a Research Retrospective," by Jarrod McClean, Staff Research Scientist at Google's Quantum Artificial Intelligence lab.  ...  As with the other articles in this issue, Baker highlights the importance of working across scientific communities to solve pressing challenges.  ... 
doi:10.1109/mcse.2021.3124033 fatcat:kw3gvcwhjfeyplwa7kj76x4dci
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