Efficient algorithms to explore conformation spaces of flexible protein loops

A. Dhanik; P. Yao; N. Marz; R. Propper; C. Kou; Guanfeng Liu; H. Van Den Bedem; J. C. Latombe

doi:10.1007/978-3-540-74126-8_25

Efficient algorithms to explore conformation spaces of flexible protein loops

A. Dhanik, P. Yao, N. Marz, R. Propper, C. Kou, Guanfeng Liu, H. Van Den Bedem, J. C. Latombe

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding contribution › peer-review

5 Citations (Scopus)

Abstract

Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples conformations broadly distributed over this space, while the "deformation sampling" algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.

Original language	English
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Place of Publication	Los Alamitos, CA
Publisher	Springer, Springer Nature
Pages	265-276
Number of pages	12
ISBN (Print)	9783540741251
DOIs	https://doi.org/10.1007/978-3-540-74126-8_25
Publication status	Published - 2007
Externally published	Yes
Event	International Workshop on Algorithms in Bioinformatics - Philadelphia, PA Duration: 8 Sept 2007 → 9 Sept 2007

Workshop

Workshop	International Workshop on Algorithms in Bioinformatics
City	Philadelphia, PA
Period	8/09/07 → 9/09/07

Access to Document

10.1007/978-3-540-74126-8_25

Cite this

Dhanik, A., Yao, P., Marz, N., Propper, R., Kou, C., Liu, G., Van Den Bedem, H., & Latombe, J. C. (2007). Efficient algorithms to explore conformation spaces of flexible protein loops. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 265-276). Springer, Springer Nature. https://doi.org/10.1007/978-3-540-74126-8_25

@inproceedings{8a63658a21724047b89c68799814e8fe,

title = "Efficient algorithms to explore conformation spaces of flexible protein loops",

abstract = "Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The {"}seed sampling{"} algorithm samples conformations broadly distributed over this space, while the {"}deformation sampling{"} algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.",

author = "A. Dhanik and P. Yao and N. Marz and R. Propper and C. Kou and Guanfeng Liu and {Van Den Bedem}, H. and Latombe, {J. C.}",

year = "2007",

doi = "10.1007/978-3-540-74126-8_25",

language = "English",

isbn = "9783540741251",

pages = "265--276",

booktitle = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer, Springer Nature",

address = "United States",

note = "International Workshop on Algorithms in Bioinformatics ; Conference date: 08-09-2007 Through 09-09-2007",

}

Dhanik, A, Yao, P, Marz, N, Propper, R, Kou, C, Liu, G, Van Den Bedem, H & Latombe, JC 2007, Efficient algorithms to explore conformation spaces of flexible protein loops. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer, Springer Nature, Los Alamitos, CA, pp. 265-276, International Workshop on Algorithms in Bioinformatics, Philadelphia, PA, 8/09/07. https://doi.org/10.1007/978-3-540-74126-8_25

Efficient algorithms to explore conformation spaces of flexible protein loops. / Dhanik, A.; Yao, P.; Marz, N. et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Los Alamitos, CA: Springer, Springer Nature, 2007. p. 265-276.

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding contribution › peer-review

TY - GEN

T1 - Efficient algorithms to explore conformation spaces of flexible protein loops

AU - Dhanik, A.

AU - Yao, P.

AU - Marz, N.

AU - Propper, R.

AU - Kou, C.

AU - Liu, Guanfeng

AU - Van Den Bedem, H.

AU - Latombe, J. C.

PY - 2007

Y1 - 2007

N2 - Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples conformations broadly distributed over this space, while the "deformation sampling" algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.

AB - Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples conformations broadly distributed over this space, while the "deformation sampling" algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.

U2 - 10.1007/978-3-540-74126-8_25

DO - 10.1007/978-3-540-74126-8_25

M3 - Conference proceeding contribution

SN - 9783540741251

SP - 265

EP - 276

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

PB - Springer, Springer Nature

CY - Los Alamitos, CA

T2 - International Workshop on Algorithms in Bioinformatics

Y2 - 8 September 2007 through 9 September 2007

ER -

Efficient algorithms to explore conformation spaces of flexible protein loops

Abstract

Workshop

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