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BMCBI
2004
208views more  BMCBI 2004»
12 years 5 months ago
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
Background: Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction...
Vadim Alexandrov, Mark Gerstein
BMCBI
2005
119views more  BMCBI 2005»
12 years 5 months ago
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Background: We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a q...
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
BMCBI
2008
109views more  BMCBI 2008»
12 years 6 months ago
The meaning of alignment: lessons from structural diversity
Background: Protein structural alignment provides a fundamental basis for deriving principles of functional and evolutionary relationships. It is routinely used for structural cla...
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
BMCBI
2007
142views more  BMCBI 2007»
12 years 6 months ago
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
Juliana S. Bernardes, Alberto M. R. Dávila,...
CSB
2004
IEEE
208views Bioinformatics» more  CSB 2004»
12 years 9 months ago
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures
Motivation: Since the whole genome sequences for many species are currently available, computational predictions of RNA secondary structures and computational identifications of t...
Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara
COMPLIFE
2005
Springer
12 years 11 months ago
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization
During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignmen...
Markus Bauer, Gunnar W. Klau, Knut Reinert
WABI
2007
Springer
13 years 2 days ago
Topology Independent Protein Structural Alignment
Abstract. Protein structural alignment is an indispensable tool used for many diļ¬€erent studies in bioinformatics. Most structural alignment algorithms assume that the structural ...
Joe Dundas, T. Andrew Binkowski, Bhaskar DasGupta,...
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