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RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
TLDR
We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. Expand
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A divide and conquer approach to fast loop modeling.
We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables,Expand
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CyloFold: secondary structure prediction including pseudoknots
TLDR
We present a computational method for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity and a test is made for steric feasibility. Expand
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The SSEA server for protein secondary structure alignment
TLDR
SUMMARY We present a web server that computes alignments of protein secondary structures. Expand
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MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification.
We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the foldExpand
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CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
TLDR
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. Expand
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Implementing Genetic Algorithms with Sterical Constraints for Protein Structure Prediction
TLDR
We present new kinds of genetic operators for protein structure prediction that restrict the search space to collision-free conformations by enforcing sterical constraints on the protein at each optimization step. Expand
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Restore: an R of sustainability that can tame the\conundrum"
The environmental benefits of sustainability efforts can be rendered less effective due to economic feedback mechanisms. As a remedy against such rebound effects, a reinvestment strategy towardsExpand
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A scoring function for docking ligands to low‐resolution protein structures
TLDR
We present a docking method that uses a scoring function for protein–ligand docking that is designed to maximize the docking success rate for low‐resolution protein structures. Expand
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Visualization of fast energy flow and solvent caging in unimolecular dynamics
ENERGY flow in solution between physically or chemically evolving solute molecules and the surrounding solvent significantly affects the nature of chemical dynamics in liquids. It determines theExpand
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