NDLI: Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

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Issue 4, October 2008

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Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics

Improving Strand Pairing Prediction through Exploring Folding Cooperativity

SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage

Seeded Tree Alignment

An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem

Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Learning Scoring Schemes for Sequence Alignment from Partial Examples

Efficient Algorithms for the Computational Design of Optimal Tiling Arrays

Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes

Gene Expression Data Analysis Using a Novel Approach to Biclustering Combining Discrete and Continuous Data

An Introduction to Metabolic Networks and Their Structural Analysis

The Undirected Incomplete Perfect Phylogeny Problem

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Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Content Provider	ACM Digital Library
Author	Altman, Russ B. Yao, Peggy Dhanik, Ankur Propper, Ryan Halperin-landsberg, Inbal Liu, Guanfeng Kou, Charles Van den bedem, Henry Latombe, Jean-Claude Marz, Nathan
Abstract	Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples broadly from this space, while the "deformation sampling" algorithm uses seed conformations as starting points to explore the conformation space around them at a finer grain. Computational results are presented for various loops ranging from 5 to 25 residues. More specific results also show that the combination of the sampling algorithms with a functional site prediction software (FEATURE) makes it possible to compute and recognize calcium-binding loop conformations. The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk.
Starting Page	534
Ending Page	545
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2008.96
Volume Number	5
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2008-10-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biology and genetics, Robotics
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Fast Hinge Detection Algorithms for Flexible Protein Structures

Efficient Algorithms for the Computational Design of Optimal Tiling Arrays

Efficient Extraction of Protein-Protein Interactions from Full-Text Articles

Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics

Selection and flexible optimization of binding modes from conformation ensembles.

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

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