Embedding graphs in books: a layout problem with applications to VLSI design
SIAM Journal on Algebraic and Discrete Methods
The pagenumber of genus g graphs is O(g)
Journal of the ACM (JACM)
On the approximation of protein threading
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
A polyhedral approach to RNA sequence structure alignment
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Computing similarity between RNA strings
Computing similarity between RNA strings
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Edit distance between two RNA structures
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Structural alignment of large—size proteins via lagrangian relaxation
Proceedings of the sixth annual international conference on Computational biology
The longest common subsequence problem for sequences with nested arc annotations
Journal of Computer and System Sciences - Computational biology 2002
The Longest Common Subsequence Problem for Sequences with Nested Arc Annotations
ICALP '01 Proceedings of the 28th International Colloquium on Automata, Languages and Programming,
Pattern Matching Problems over 2-Interval Sets
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
The Longest Common Subsequence Problem for Arc-Annotated Sequences
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
A Study on the use of "self-generation'' in memetic algorithms
Natural Computing: an international journal
Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case
Genetic Programming and Evolvable Machines
Integer programming models for computational biology problems
Journal of Computer Science and Technology - Special issue on bioinformatics
A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fréchet distance for curves, revisited
ESA'06 Proceedings of the 14th conference on Annual European Symposium - Volume 14
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Approximating the 2-interval pattern problem
Theoretical Computer Science
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
On two open problems of 2-interval patterns
Theoretical Computer Science
On Protein Structure Alignment under Distance Constraint
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
Bimal: bipartite matching alignment for the contact map overlap problem
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Multiple alignment of contact maps
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Geometric suffix tree: Indexing protein 3-D structures
Journal of the ACM (JACM)
A fuzzy sets based generalization of contact maps for the overlap of protein structures
Fuzzy Sets and Systems
The Journal of Machine Learning Research
Joining softassign and dynamic programming for the contact map overlap problem
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Comparing RNA structures: towards an intermediate model between the edit and the LAPCS problems
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
Protein structure alignment using maximum cliques and local search
AI'07 Proceedings of the 20th Australian joint conference on Advances in artificial intelligence
Finding common structured patterns in linear graphs
Theoretical Computer Science
Linear-time protein 3-D structure searching with insertions and deletions
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
On protein structure alignment under distance constraint
Theoretical Computer Science
Optimizing a Widely Used Protein Structure Alignment Measure in Expected Polynomial Time
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Finding common RNA pseudoknot structures in polynomial time
Journal of Discrete Algorithms
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the complexity of the crossing contact map pattern matching problem
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Finding common RNA pseudoknot structures in polynomial time
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
RNA multiple structural alignment with longest common subsequences
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
On Complexity of Protein Structure Alignment Problem under Distance Constraint
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
What makes the arc-preserving subsequence problem hard?
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Fast protein structure alignment
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
What makes the arc-preserving subsequence problem hard?
Transactions on Computational Systems Biology II
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SHREC'10 track: protein model classification
EG 3DOR'10 Proceedings of the 3rd Eurographics conference on 3D Object Retrieval
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
DALIX: Optimal DALI Protein Structure Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
| Hi-index | 0.01 |
We show that calculating contact map overlap (a measure of similarity of protein structures) is NP-hard, but can be solved in polynomial time for several interesting and relevant special cases. We identify an important special case of this problem corresponding to self-avoiding walks, and prove a decomposition theorem and a corollary approximation result for this special case. These are the first approximation algorithms with guaranteed error bounds, and NP-completeness results in the literature in the area of protein structure alignment/fold recognition for measures of structure similarity of practical interest.