@article {Gront2006, title = {BioShell{\textendash}a package of tools for structural biology computations}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {5}, year = {2006}, month = {mar}, pages = {621{\textendash}622}, abstract = {

SUMMARY: BioShell is a suite of programs performing common tasks accompanying protein structure modeling. BioShell design is based on UNIX shell flexibility and should be used as its extension. Using BioShell various molecular modeling procedures can be integrated in a single pipeline. AVAILABILITY: BioShell package can be downloaded from its website http://biocomp.chem.uw.edu.pl/BioShell and these pages provide many examples and a detailed documentation for the newest version.

}, keywords = {Chemical, Computational Biology, Computational Biology: methods, Computer Simulation, Databases, Models, Protein, Protein: methods, Proteins, Proteins: analysis, Proteins: chemistry, Proteins: classification, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btk037}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16407320}, author = {Dominik Gront and Andrzej Koli{\'n}ski} } @article {Gront2005, title = {HCPM{\textendash}program for hierarchical clustering of protein models}, journal = {Bioinformatics}, volume = {21}, number = {14}, year = {2005}, pages = {3179{\textendash}80}, abstract = {HCPM is a tool for clustering protein structures from comparative modeling, ab initio structure prediction, etc. A hierarchical clustering algorithm is designed and tested, and a heuristic is provided for an optimal cluster selection. The method has been successfully tested during the CASP6 experiment.}, keywords = {Algorithms, Chemical, Cluster Analysis, Computer Simulation, Internet, Models, Molecular, Protein, Protein: methods, Proteins, Proteins: analysis, Proteins: chemistry, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, User-Computer Interface}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bti450}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15840705}, author = {Dominik Gront and Andrzej Koli{\'n}ski} } @article {Gront2005a, title = {A new approach to prediction of short-range conformational propensities in proteins}, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {7}, year = {2005}, pages = {981{\textendash}987}, abstract = {

MOTIVATION: Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data. RESULTS: A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.

}, keywords = {Algorithms, Amino Acid, Artificial Intelligence, Chemical, Computer Simulation, Databases, Gas Chromatography-Mass Spectrometry, Gas Chromatography-Mass Spectrometry: methods, Models, Protein, Protein Conformation, Protein: methods, Proteins, Proteins: analysis, Proteins: chemistry, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Sequence Homology, Structure-Activity Relationship}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bti080}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15509604}, author = {Dominik Gront and Andrzej Koli{\'n}ski} }