Refining multiple sequence alignments with conserved core regions

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution () and will be incorporated into the next release of the Cn3D structure/alignment viewer

A one-dimensional model for the growth of CdTe quantum dots on Si substrates

Recent experiments involving CdTe films grown on Si(111) substrates by hot wall epitaxy revealed features not previously observed [S. O. Ferreira \textit{et al.}, J. Appl. Phys. \textbf{93}, 1195 (2003)]. This system, which follows the Volmer-Weber growth mode with nucleation of isolated 3D islands for less than one monolayer of evaporated material, was described by a peculiar behavior of the quantum dot (QD) size distributions. In this work, we proposed a kinetic deposition model to reproduce these new features. The model, which includes thermally activated diffusion and evaporation of CdTe, qualitatively reproduced the experimental QD size distributions. Moreover, the model predicts a transition from Stranski-Krastanow growth mode at lower temperatures to Volmer-Weber growth mode at higher ones characterized through the QD width distributions.Comment: to appear in Physics Letters

Impurity-induced diffusion bias in epitaxial growth

We introduce two models for the action of impurities in epitaxial growth. In the first, the interaction between the diffusing adatoms and the impurities is ``barrier''-like and, in the second, it is ``trap''-like. For the barrier model, we find a symmetry breaking effect that leads to an overall down-hill current. As expected, such a current produces Edwards-Wilkinson scaling. For the trap model, no symmetry breaking occurs and the scaling behavior appears to be of the conserved-KPZ type.Comment: 5 pages(with the 5 figures), latex, revtex3.0, epsf, rotate, multico

A Simple Model for Anisotropic Step Growth

We consider a simple model for the growth of isolated steps on a vicinal crystal surface. It incorporates diffusion and drift of adatoms on the terrace, and strong step and kink edge barriers. Using a combination of analytic methods and Monte Carlo simulations, we study the morphology of growing steps in detail. In particular, under typical Molecular Beam Epitaxy conditions the step morphology is linearly unstable in the model and develops fingers separated by deep cracks. The vertical roughness of the step grows linearly in time, while horizontally the fingers coarsen proportional to $t^{0.33}$. We develop scaling arguments to study the saturation of the ledge morphology for a finite width and length of the terrace.Comment: 20 pages, 12 figures; [email protected]

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure

Instabilities in crystal growth by atomic or molecular beams

The planar front of a growing a crystal is often destroyed by instabilities. In the case of growth from a condensed phase, the most frequent ones are diffusion instabilities, which will be but briefly discussed in simple terms in chapter II. The present review is mainly devoted to instabilities which arise in ballistic growth, especially Molecular Beam Epitaxy (MBE). The reasons of the instabilities can be geometric (shadowing effect), but they are mostly kinetic or thermodynamic. The kinetic instabilities which will be studied in detail in chapters IV and V result from the fact that adatoms diffusing on a surface do not easily cross steps (Ehrlich-Schwoebel or ES effect). When the growth front is a high symmetry surface, the ES effect produces mounds which often coarsen in time according to power laws. When the growth front is a stepped surface, the ES effect initially produces a meandering of the steps, which eventually may also give rise to mounds. Kinetic instabilities can usually be avoided by raising the temperature, but this favours thermodynamic instabilities. Concerning these ones, the attention will be focussed on the instabilities resulting from slightly different lattice constants of the substrate and the adsorbate. They can take the following forms. i) Formation of misfit dislocations (chapter VIII). ii) Formation of isolated epitaxial clusters which, at least in their earliest form, are `coherent' with the substrate, i.e. dislocation-free (chapter X). iii) Wavy deformation of the surface, which is presumably the incipient stage of (ii) (chapter IX). The theories and the experiments are critically reviewed and their comparison is qualitatively satisfactory although some important questions have not yet received a complete answer.Comment: 90 pages in revtex, 45 figures mainly in gif format. Review paper to be published in Physics Reports. Postscript versions for all the figures can be found at http://www.theo-phys.uni-essen.de/tp/u/politi

CDD: a Conserved Domain Database for protein classification

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system