We present a computational pipeline to predict cis-regulatory elements composing results based on different algorithms: Clover, Cluster-Buster, an own implementation of human/rat/mouse sequence identity and our ITB algorithm. The procedure uses information from the human genome sequence, NCBI gene

Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was applied to determine the core cell cycle genes in the recently completed Arabidopsis genome

Abstract: The goal of computational protein structure prediction is to provide three-dimensional (3D) structures with resolution comparable to experimental results. Comparative modeling, which predicts the 3D structure of a protein based on its sequence similarity to homologous structures

beryllofluoride was selected as the optimal template for modeling a SpaK/SpaR complex conformation. In vitro phosphorylation studies performed using wild type and site-directed SpaK mutant proteins validated the predictions derived from application of the structure-driven domain-fusion method: Spa

of anesthetics with the microtubule subunit protein tubulin is investigated using computer-modeling methods. Homology modeling, molecular dynamics simulations and surface geometry techniques were used to determine putative binding sites for volatile anesthetics on tubulin. This was followed by free energy based

domains. Two mannose 6-phosphate (M6P) binding sites have been mapped to domains 3 and 9, whereas domain 5 binds preferentially to the phosphodiester, M6P-N-acetylglucosamine (GlcNAc). A structure-based sequence alignment predicts that the C-terminal domain 15 contains three out of the four conserved

-ATPase. The homology suggests a new domain structure for Ca21-ATPase and, specifically, that the phosphorylation domain adopts a Rossman fold. Accordingly, the atomic structure of L-2 haloacid dehalogenase has been fitted into the relevant domain of Ca21-ATPase. The resulting model suggests the existence

muscle. Alignment analysis revealed that the deduced protein sequence shares 86%, 91 % and 93 % homology with that of its human, mouse and rat counterparts, respectively. The LMCD1 protein was predicted by bioinformatics software to contain a novel cysteine-rich domain in the N-terminal region, two LIM

924361 and SRR924427. We conducted homology-based gene prediction and identified 20,424 genes for R. ferrumequinum, 20,043 for M. lyra, 20,455 for E. helvum and 20,357 for P. parnellii. Screening for single-copy (1-to-1) orthologous protein-coding nuclear genes conserved across eutherian mammals

predicted consensus casein kinase II phosphorylation site and a hydrophobic secretory signal peptide, but did not have glycosylation sites. The Ab-FAR-1 had 52 % homology to Gp-FAR-1 protein. The Ab-FAR-1 and Gp-FAR-1 were grouped in the same branch according to the phylogenetic tree. Fluorescence-based