Least-Squares Fitting of Two 3-D Point Sets
IEEE Transactions on Pattern Analysis and Machine Intelligence
Least-Squares Estimation of Transformation Parameters Between Two Point Patterns
IEEE Transactions on Pattern Analysis and Machine Intelligence
Smoothing and matching of 3-D space curves
International Journal of Computer Vision
Multiple Structural Alignment and Core Detection by Geometric Hashing
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
An Efficient Index-based Protein Structure Database Searching Method
DASFAA '03 Proceedings of the Eighth International Conference on Database Systems for Advanced Applications
Comparing 3D Protein Structures Similarity by Using Fractal Features
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Protein structure alignment using geometrical features
Proceedings of the thirteenth ACM international conference on Information and knowledge management
PSIST: Indexing Protein Structures Using Suffix Trees
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
PSIST: A scalable approach to indexing protein structures using suffix trees
Journal of Parallel and Distributed Computing
On Using Energy Signatures in Protein Structure Similarity Searching
ICAISC '08 Proceedings of the 9th international conference on Artificial Intelligence and Soft Computing
PSISA: an algorithm for indexing and searching protein structure using suffix arrays
ICCOMP'08 Proceedings of the 12th WSEAS international conference on Computers
Agent-Supported Protein Structure Similarity Searching
Agent Computing and Multi-Agent Systems
DDPIn: distance and density based protein indexing
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Geometric suffix tree: Indexing protein 3-D structures
Journal of the ACM (JACM)
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
EAST: energy alignment search tool
FSKD'06 Proceedings of the Third international conference on Fuzzy Systems and Knowledge Discovery
Geometric suffix tree: a new index structure for protein 3-d structures
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
PADS: protein structure alignment using directional shape signatures
DASFAA'05 Proceedings of the 10th international conference on Database Systems for Advanced Applications
Efficient Approaches for Retrieving Protein Tertiary Structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Protein motifs retrieval by SS terns occurrences
Pattern Recognition Letters
| Hi-index | 0.00 |
We present a new method for conducting proteinstructure similarity searches, which improves on theaccuracy, robustness, and efficiency of some existingtechniques. Our method is grounded in the theory ofdifferential geometry on 3D space curve matching. Wegenerate shape signatures for proteins that areinvariant, localized, robust, compact, and biologicallymeaningful. To improve matching accuracy, we smooththe noisy raw atomic coordinate data with spline fitting.To improve matching efficiency, we adopt a hierarchicalcoarse-to-fine strategy. We use an efficient hashing-basedtechnique to screen out unlikely candidates andperform detailed pairwise alignments only for a smallnumber of candidates that survive the screening process.Contrary to other hashing based techniques, ourtechnique employs domain specific information (not justgeometric information) in constructing the hash key, andhence, is more tuned to the domain of biology.Furthermore, the invariancy, localization, andcompactness of the shape signatures allow us to utilize awell-known local sequence alignment algorithm foraligning two protein structures. One measure of theefficacy of the proposed technique is that we were ableto discover new, meaningful motifs that were notreported by other structure alignment methods.