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An algorithm with linear complexity for interactive, physically-based modeling of large proteins

Author:

Mark C. SurlesAuthors Info & Claims

ACM SIGGRAPH Computer Graphics, Volume 26, Issue 2

Pages 221 - 230

https://doi.org/10.1145/142920.134065

Published: 01 July 1992 Publication History

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References

[1]

Akeley, K. and Jermoluk, T. High-Performance Polygon Rendering. Computer Graphics. 22, 4 (1988), 239-246.]]

Digital Library

Google Scholar

[2]

Bentley, J. L. and Friedman, J. H. Data Structures for Range Searching. Computing Surveys. I 1, 4 (1979), 397-409.]]

Digital Library

Google Scholar

[3]

Insight. Biosym Technologies Inc., 1991.]]

Google Scholar

[4]

Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. Journal of Computational Chemistry. 4, 2 (1983), 187-217.]]

Crossref

Google Scholar

[5]

Duff, I. S., Erisman, A. M. and Reid, J. K. Direct Methods for Sparse Matrices. Clarendon Press, Oxford, 1986.]]

Digital Library

Google Scholar

[6]

Fletcher, R. Practical Methods of Optimization. John Wiley and Sons, 1987.]]

Digital Library

Google Scholar

[7]

Gill, P., Murray, W. and Wright, M. Practical Optimization. Academic Press, 1981.]]

Google Scholar

[8]

Hecht, M. H., Richardson, J. S., Richardson, D. C. and Ogden, R. C. De Novo Design, Expression, and Characterization of Felix: A Four-Helix Bundle Protein of Native-Like Sequence. Science. 249, 4964 (1990), 884-891.]]

Crossref

Google Scholar

[9]

Hestenes, M. R. Optimization Theory, The Finite Dimensional Case. John Wiley and Sons, New York, 1975.]]

Google Scholar

[10]

Knuth, D. E. Fundamental Algorithms, The Art of Computer Programming. Addison-Wesley, 1973.]]

Digital Library

Google Scholar

[11]

Levinthal, C. Molecular Model-building by Computer. Scienn'fic American. 214, 6 (1966).]]

Crossref

Google Scholar

[12]

Luenberger, D. G. Introduction to Linear and Nonlinear Programming. Addison-Wesley, 1973.]]

Google Scholar

[13]

Pentland, A. and Williams, J. Good Vibrations: Modal Dynamics for Graphics and Animation. Computer Graphics. 23, 3 (1989), 215-222.]]

Digital Library

Google Scholar

[14]

Platt, J. Constraint Methods for Neural Networks and Computer Graphics. Ph.D. Dissertation, California Institute of Technology, 1989.]]

Digital Library

Google Scholar

[15]

Platt, J. and Barr, A. Constraint Methods for Flexible Models. Computer Graphics. 22, 4 (1988), 279-288.]]

Digital Library

Google Scholar

[16]

Quanta. Polygen Corporation, 1991.]]

Google Scholar

[17]

Schulz, G. E. and Schirmer, R. H. Principles of Protein Structure. Springer-Verlag, New York, 1979.]]

Crossref

Google Scholar

[18]

Stroustrup, B. The C+ + Programming Language. Addison- Wesley, 1986.]]

Digital Library

Google Scholar

[19]

Surles, M. Interactive Modeling Enhanced with Constraints and PhysicslWith Applications in Molecular Modeling. Symposium on Interactive 3D Graphics. 26, 2 (i 992), 175- 182.]]

Digital Library

Google Scholar

[20]

Surles, M. Techniques For Interactive Manipulation of Graphical Protein Models. Ph.D. Dissertation, University of North Carolina at Chapel Hill, 1992.]]

Digital Library

Google Scholar

[21]

Terzopoulos, D. and Fleischer, K. Modeling Inelastic Deformation: Viscoelasticity, Plasticity, Fracture. Computer Graphics. 22, 4 (1988), 269-278.]]

Digital Library

Google Scholar

[22]

Sybyl. Tripos Associates, 1988.]]

Google Scholar

[23]

Weiner, S. J., Kollman, P. A., Case, D. A., Singh, C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P. A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins. Journal of the American Chemical Society. 106, (1984), 765-784.]]

Crossref

Google Scholar

[24]

Witkin, A., Gleicher, M. and Welch, W. Interactive Dynamics. Symposium on Interactive 3D Graphics. 24, 2 (1990), 11-21.]]

Digital Library

Google Scholar

[25]

Witkin, A. and Welch, W. Fast Animation and Control of Nonrigid Structures. Computer Graphics. 24, 4 (1990), 243- 252.]]

Digital Library

Google Scholar

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Lamiraux FKavraki L(2016)Planning Paths for Elastic Objects under Manipulation ConstraintsThe International Journal of Robotics Research10.1177/0278364012206735420:3(188-208)Online publication date: 2-Jul-2016
https://doi.org/10.1177/02783640122067354
Brenner SBerry A(2008)A quantitative methodology for the de novo design of proteinsProtein Science10.1002/pro.55600310263:10(1871-1882)Online publication date: 31-Dec-2008
https://doi.org/10.1002/pro.5560031026
Surles MRichardson JRichardson DBrooks F(2008)Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling systemProtein Science10.1002/pro.55600302053:2(198-210)Online publication date: 31-Dec-2008
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An algorithm with linear complexity for interactive, physically-based modeling of large proteins

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Published In

cover image ACM SIGGRAPH Computer Graphics

ACM SIGGRAPH Computer Graphics Volume 26, Issue 2

July 1992

366 pages

ISSN:0097-8930

DOI:10.1145/142920

Editor:
Maxine Brown
Univ. of Illinois at Chicago

Issue’s Table of Contents

SIGGRAPH '92: Proceedings of the 19th annual conference on Computer graphics and interactive techniques
July 1992
420 pages
ISBN:0897914791
DOI:10.1145/133994
Editor:
James J. Thomas
Battelle Pacific Northwest Labs, Richland, WA

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

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Publication History

Published: 01 July 1992

Published in SIGGRAPH Volume 26, Issue 2

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Cited By

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Lamiraux FKavraki L(2016)Planning Paths for Elastic Objects under Manipulation ConstraintsThe International Journal of Robotics Research10.1177/0278364012206735420:3(188-208)Online publication date: 2-Jul-2016
https://doi.org/10.1177/02783640122067354
Brenner SBerry A(2008)A quantitative methodology for the de novo design of proteinsProtein Science10.1002/pro.55600310263:10(1871-1882)Online publication date: 31-Dec-2008
https://doi.org/10.1002/pro.5560031026
Surles MRichardson JRichardson DBrooks F(2008)Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling systemProtein Science10.1002/pro.55600302053:2(198-210)Online publication date: 31-Dec-2008
https://doi.org/10.1002/pro.5560030205
Lee DBae HTae Kim CLee DJung DLee NLee KBaek NWon Lee JWoo Ryu KHahn J(2001)Reproducing works of CalderThe Journal of Visualization and Computer Animation10.1002/vis.24712:2(81-91)Online publication date: 11-Jun-2001
https://doi.org/10.1002/vis.247
Dachille FQin HKaufman AEl-Sana JRossignac JHodgins JFoley J(1999)Haptic sculpting of dynamic surfacesProceedings of the 1999 symposium on Interactive 3D graphics10.1145/300523.300535(103-110)Online publication date: 26-Apr-1999
https://dl.acm.org/doi/10.1145/300523.300535
Olson APique M(1998)Visualizing The Future of Molecular GraphicsSAR and QSAR in Environmental Research10.1080/106293698080391428:3-4(233-247)Online publication date: Jan-1998
https://doi.org/10.1080/10629369808039142
Ngo JKarplus M(1997)Pseudosystematic Conformational Search. Application to CycloheptadecaneJournal of the American Chemical Society10.1021/ja961132o119:24(5657-5667)Online publication date: 18-Jun-1997
https://doi.org/10.1021/ja961132o
Baraff DFujii J(1996)Linear-time dynamics using Lagrange multipliersProceedings of the 23rd annual conference on Computer graphics and interactive techniques10.1145/237170.237226(137-146)Online publication date: 1-Aug-1996
https://dl.acm.org/doi/10.1145/237170.237226
Berger PBidart JDelves PDirnhofer SHoermann RIsaacs NJackson AKlonisch TLapthorn ALund TMann KRoitt ISchwarz SWick G(1996)Immunochemical mapping of gonadotropinsMolecular and Cellular Endocrinology10.1016/S0303-7207(96)03943-3125:1-2(33-43)Online publication date: Dec-1996
https://doi.org/10.1016/S0303-7207(96)03943-3
Jones CJones C(1996)AnimationVisualization and Optimization10.1007/978-1-4615-4121-9_15(349-370)Online publication date: 1996
https://doi.org/10.1007/978-1-4615-4121-9_15
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