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At least 271 records · Page 15Linked to original sources
PubMed2005

Computational methods for remote homolog identification.

As more and more protein sequences are available, homolog identification becomes increasingly important for functional, structural, and evolutional studies of proteins. Many homologous proteins were separated a very long time ago in their evolutionary history and thus their sequences share low sequence identity. These remote homologs have become a research focus in bioinformatics over the past decade, and some significant advances have been achieved. In this paper, we provide a comprehensive review on computational techniques used in remote homolog identification based on different methods, including sequence-sequence comparison, and sequence-structure comparison, and structure-structure comparison. Other miscellaneous approaches are also summarized. Pointers to the online resources of these methods and their related databases are provided. Comparisons among different methods in terms of their technical approaches, their strengths, and limitations are followed. Studies on proteins in SARS-CoV are shown as an example for remote homolog identification application.

Animals↗
PubMed2004

Computational methods for the identification and optimisation of high quality leads.

Lead identification and optimisation have evolved into multidimensional, multidisciplinary and information-driven processes. Herein, we review the contribution of computational chemistry to these processes. We focus on computational approaches developed for modelling biopharmaceutical properties, including in vitro activity, selectivity, absorption, distribution, metabolism, excretion and toxicity. Whenever possible, successful applications are mentioned.

Animals↗
PubMed2005

Determining localized garment insulation values from manikin studies: computational method and results.

The localized thermal insulation value expresses a garment's thermal resistance over the region which is covered by the garment, rather than over the entire surface of a subject or manikin. The determination of localized garment insulation values is critical to the development of high-resolution models of sensible heat exchange. A method is presented for determining and validating localized garment insulation values, based on whole-body insulation values (clo units) and using computer-aided design and thermal analysis software. Localized insulation values are presented for a catalog consisting of 106 garments and verified using computer-generated models. The values presented are suitable for use on volume element-based or surface element-based models of heat transfer involving clothed subjects.

Body Temperature Regulation↗
PubMedDate not supplied

Characterization of the conformational domains of bradykinin by computational methods.

The AMBER 4.0 force field was used to perform a characterization of the conformational profile of the nonapeptide bradykinin. A thorough conformational search was carried out using molecular dynamics as sampling technique, by computing cycles of high (900 K) and low (300 K) temperature trajectories. A total of 2400 minima were generated and subsequently clustered using the root-mean-square of the backbone dihedral angles as criterium. After the use of a tolerance value of 20 degrees, the conformations were clustered in 233 unique conformations with energies up to 40 kcal/mol above the lowest minimum. The analysis of the low-energy conformations indicate that the peptide exhibits a high tendency to adopt a beta-turn at the C-terminus and a propensity to adopt a bent structure at the N-terminus. These results are in agreement with the experimental evidence reported in the literature and provide detailed information necessary to understand the conformational preferences of the peptide.

Amino Acid Sequence↗
PubMed2002

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

Algorithms↗
PubMed1991

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗