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BMCBI
2010
154views more  BMCBI 2010»
14 years 11 months ago
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
Background: Modelling the ligand binding site of a protein is an important component of understanding proteinligand interactions and is being actively studied. Even if the side ch...
Edon Sung, Sangsoo Kim, Whanchul Shin
BMCBI
2008
111views more  BMCBI 2008»
14 years 11 months ago
A perl package and an alignment tool for phylogenetic networks
Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombin...
Gabriel Cardona, Francesc Rosselló, Gabriel...
BMCBI
2004
208views more  BMCBI 2004»
14 years 11 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
2004
133views more  BMCBI 2004»
14 years 11 months ago
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Background: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily co...
Robin D. Dowell, Sean R. Eddy
PODC
2004
ACM
15 years 4 months ago
Analyzing Kleinberg's (and other) small-world Models
We analyze the properties of Small-World networks, where links are much more likely to connect “neighbor nodes” than distant nodes. In particular, our analysis provides new re...
Charles U. Martel, Van Nguyen