In molecular databases, structural classification is a basic task that can be successfully approached by nearest neighbor methods. The underlying similarity models consider spatial properties such as shape and extension as well as thematic attributes. We introduce 3D shape histograms as an intuitive and powerful approach to model similarity for solid objects such as molecules. Errors of measure...

Protein crystallization plays a crucial role in pharmaceutical research by supporting the investigation of a protein’s molecular structure through X-ray diffraction of its crystal. Due to the rare occurrence of crystals, images must be manually inspected, a laborious process. We develop a solution incorporating a regularized, logistic regression model for automatically evaluating these images. ...

The phylogenomic classification of protein sequences attempts to categorize a given protein within the evolutionary context of the entire family. It involves mainly four steps: selection of homologous sequences, multiple sequence alignment, phylogenetic tree construction and tree-based classification. This supposes that the tree used as a basis of protein classification is correct. Sequence ali...

Departments of Biology and *Cell Biology and Anatomy, Johns Hopkins University, Baltimore, Maryland 21218; ¢Departments of Cell Biology and Physiology and of Genetics, Washington University School of Medicine, St. Louis, Missouri 63310; § Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; and II Department of Biological Chemistry, University of California at Los Angeles School o...

With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR prod...

The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a...

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the sta...

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of...