Learn More
We have modified and improved the GOR algorithm for the protein secondary structure prediction by using the evolutionary information provided by multiple sequence alignments, adding triplet statistics, and optimizing various parameters. We have expanded the database used to include the 513 non-redundant domains collected recently by Cuff and Barton(More)
One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database(More)
The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the(More)
The elastic network interpolation (ENI) (Kim et al., Biophys J 2002;83:1620-1630) is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this(More)
Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number(More)
SUMMARY We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful(More)
A new method for predicting protein secondary structure from amino acid sequence has been developed. The method is based on multiple sequence alignment of the query sequence with all other sequences with known structure from the protein data bank (PDB) by using BLAST. The fragments of the alignments belonging to proteins from the PBD are then used for(More)
The major aim of tertiary structure prediction is to obtain protein models with the highest possible accuracy. Fold recognition, homology modeling, and de novo prediction methods typically use predicted secondary structures as input, and all of these methods may significantly benefit from more accurate secondary structure predictions. Although there are(More)
Two-body inter-residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are(More)
A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of(More)