Geometric manipulation of flexible ligands

Paul W. Finn; Dan Halperin; Lydia E. Kavraki; Jean Claude Latombe; Rajeev Motwani; Christian Shelton; Suresh Venkatasubramanian

doi:10.1007/bfb0014486

Geometric manipulation of flexible ligands

Paul W. Finn, Dan Halperin, Lydia E. Kavraki, Jean Claude Latombe, Rajeev Motwani, Christian Shelton, Suresh Venkatasubramanian

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

Abstract

In recent years an effort has been made to supplement traditional methods for drug discovery by computer-assisted “structure-based design.” The structure-based approach involves (among other issues) reasoning about the geometry of drug molecules (or ligands) and about the different spatial conformations that these molecules can attain. This is a preliminary report on a set of tools that we are devising to assist the chemist in the drug design process. We describe our work on the following three topics: (i) geometric data structures for representing and manipulating molecules; (ii) conformational analysis—searching for low- energy conformations; and (iii) pharmacophore identification—searching for common features among different ligands that exhibit similar activity.

Original language	English
Title of host publication	Applied Computational Geometry
Subtitle of host publication	Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers
Editors	Ming C. Lin, Ming C. Lin, Dinesh Manocha
Publisher	Springer Verlag
Pages	67-78
Number of pages	12
ISBN (Print)	354061785X, 9783540617853
DOIs	https://doi.org/10.1007/bfb0014486
State	Published - 1996
Externally published	Yes
Event	1st ACM Workshop on Applied Computational Geometry, WACG 1996 held as part of 2nd Federated Computing Research Conference, FCRC 1996 - Philadelphia, United States Duration: 27 May 1996 → 28 May 1996

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	1148
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st ACM Workshop on Applied Computational Geometry, WACG 1996 held as part of 2nd Federated Computing Research Conference, FCRC 1996
Country/Territory	United States
City	Philadelphia
Period	27/05/96 → 28/05/96

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10.1007/bfb0014486

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Finn, P. W., Halperin, D., Kavraki, L. E., Latombe, J. C., Motwani, R., Shelton, C., & Venkatasubramanian, S. (1996). Geometric manipulation of flexible ligands. In M. C. Lin, M. C. Lin, & D. Manocha (Eds.), Applied Computational Geometry: Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers (pp. 67-78). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 1148). Springer Verlag. https://doi.org/10.1007/bfb0014486

Finn, Paul W. ; Halperin, Dan ; Kavraki, Lydia E. et al. / Geometric manipulation of flexible ligands. Applied Computational Geometry: Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers. editor / Ming C. Lin ; Ming C. Lin ; Dinesh Manocha. Springer Verlag, 1996. pp. 67-78 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "In recent years an effort has been made to supplement traditional methods for drug discovery by computer-assisted “structure-based design.” The structure-based approach involves (among other issues) reasoning about the geometry of drug molecules (or ligands) and about the different spatial conformations that these molecules can attain. This is a preliminary report on a set of tools that we are devising to assist the chemist in the drug design process. We describe our work on the following three topics: (i) geometric data structures for representing and manipulating molecules; (ii) conformational analysis—searching for low- energy conformations; and (iii) pharmacophore identification—searching for common features among different ligands that exhibit similar activity.",

author = "Finn, {Paul W.} and Dan Halperin and Kavraki, {Lydia E.} and Latombe, {Jean Claude} and Rajeev Motwani and Christian Shelton and Suresh Venkatasubramanian",

note = "Publisher Copyright: {\textcopyright} Springer-Verlag Berlin Heidelberg 1996.; 1st ACM Workshop on Applied Computational Geometry, WACG 1996 held as part of 2nd Federated Computing Research Conference, FCRC 1996 ; Conference date: 27-05-1996 Through 28-05-1996",

year = "1996",

doi = "10.1007/bfb0014486",

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

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Finn, PW, Halperin, D, Kavraki, LE, Latombe, JC, Motwani, R, Shelton, C & Venkatasubramanian, S 1996, Geometric manipulation of flexible ligands. in MC Lin, MC Lin & D Manocha (eds), Applied Computational Geometry: Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 1148, Springer Verlag, pp. 67-78, 1st ACM Workshop on Applied Computational Geometry, WACG 1996 held as part of 2nd Federated Computing Research Conference, FCRC 1996, Philadelphia, United States, 27/05/96. https://doi.org/10.1007/bfb0014486

Geometric manipulation of flexible ligands. / Finn, Paul W.; Halperin, Dan; Kavraki, Lydia E. et al.
Applied Computational Geometry: Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers. ed. / Ming C. Lin; Ming C. Lin; Dinesh Manocha. Springer Verlag, 1996. p. 67-78 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 1148).

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

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AB - In recent years an effort has been made to supplement traditional methods for drug discovery by computer-assisted “structure-based design.” The structure-based approach involves (among other issues) reasoning about the geometry of drug molecules (or ligands) and about the different spatial conformations that these molecules can attain. This is a preliminary report on a set of tools that we are devising to assist the chemist in the drug design process. We describe our work on the following three topics: (i) geometric data structures for representing and manipulating molecules; (ii) conformational analysis—searching for low- energy conformations; and (iii) pharmacophore identification—searching for common features among different ligands that exhibit similar activity.

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Finn PW, Halperin D, Kavraki LE, Latombe JC, Motwani R, Shelton C et al. Geometric manipulation of flexible ligands. In Lin MC, Lin MC, Manocha D, editors, Applied Computational Geometry: Towards Geometric Engineering - FCRC 1996 Workshop, WACG 1996, Selected Papers. Springer Verlag. 1996. p. 67-78. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/bfb0014486

Geometric manipulation of flexible ligands

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