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Computational Biology Support: RECOMB Conference Series (Conference Support)
This funding was support for student and postdoctoral attendance at the Annual Recomb Conference from 2001 to 2005. The RECOMB Conference series was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference series aims at attracting research contributions in all areas of computational molecular biology. Typical, but not exclusive, the topics of interest are: Genomics, Molecular sequence analysis, Recognition of genes and regulatory elements, Molecular evolution, Protein structure, Structural genomics, Gene Expression, Gene Networks, Drug Design, Combinatorial libraries, Computational proteomics, and Structural and functional genomics. The origins of the conference came from the mathematical and computational side of the field, and there remains to be a certain focus on computational advances. However, the effective use of computational techniques to biological innovation is also an important aspect of the conference. The conference had a growing number of attendees, topping 300 in recent years and often exceeding 500. The conference program includes between 30 and 40 contributed papers, that are selected by a international program committee with around 30 experts during a rigorous review process rivaling the editorial procedure for top-rate scientific journals. In previous years papers selection has been made from up to 130--200 submissions from well over a dozen countries. 10-page extended abstracts of the contributed papers are collected in a volume published by ACM Press and Springer, and are available at the conference. Full versions of a selection of the papers are published annually in a special issue of the Journal of Computational Biology devoted to the RECOMB Conference. A further point in the program is a lively poster session. From 120-300 posters have been presented each year at RECOMB 2000. One of the highlights of each RECOMB conference is a collection of nine keynotes awarded to researchers of highest international esteem who are asked to inform the community about landmark advances in computational and experimental research and inject new directions into the field of computational molecular biology. This includes the following conference events: Next we present a list of the names of the students and postdocs supported. Those supported either presented a paper (10 in 2001, 6 in 2002, 7 in 2003, 14 in 2004, and 20 in 2006) or were they presenter of a poster. This support was vital to the quality and success of the Conference. At the conclusion we give the publication details of the relevant Recomb proceedings
The Journal of Computer-Aided Molecular Design: a bibliometric note
Summarizes the articles in, and the citations to, volumes 2-24 of the Journal of Computer-Aided Molecular Design. The citations to the journal come from almost 2000 different sources that span a very wide range of academic subjects, with the most heavily cited articles being descriptions of software systems and of computational methods
Dynamic and multi-pharmacophore modeling for designing polo-box domain inhibitors.
The polo-like kinase 1 (Plk1) is a critical regulator of cell division that is overexpressed in many types of tumors. Thus, a strategy in the treatment of cancer has been to target the kinase activity (ATPase domain) or substrate-binding domain (Polo-box Domain, PBD) of Plk1. However, only few synthetic small molecules have been identified that target the Plk1-PBD. Here, we have applied an integrative approach that combines pharmacophore modeling, molecular docking, virtual screening, and in vitro testing to discover novel Plk1-PBD inhibitors. Nine Plk1-PBD crystal structures were used to generate structure-based hypotheses. A common pharmacophore model (Hypo1) composed of five chemical features was selected from the 9 structure-based hypotheses and used for virtual screening of a drug-like database consisting of 159,757 compounds to identify novel Plk1-PBD inhibitors. The virtual screening technique revealed 9,327 compounds with a maximum fit value of 3 or greater, which were selected and subjected to molecular docking analyses. This approach yielded 93 compounds that made good interactions with critical residues within the Plk1-PBD active site. The testing of these 93 compounds in vitro for their ability to inhibit the Plk1-PBD, showed that many of these compounds had Plk1-PBD inhibitory activity and that compound Chemistry_28272 was the most potent Plk1-PBD inhibitor. Thus Chemistry_28272 and the other top compounds are novel Plk1-PBD inhibitors and could be used for the development of cancer therapeutics
Chaste: an open source C++ library for computational physiology and biology
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials
10 simple rules to create a serious game, illustrated with examples from structural biology
Serious scientific games are games whose purpose is not only fun. In the
field of science, the serious goals include crucial activities for scientists:
outreach, teaching and research. The number of serious games is increasing
rapidly, in particular citizen science games, games that allow people to
produce and/or analyze scientific data. Interestingly, it is possible to build
a set of rules providing a guideline to create or improve serious games. We
present arguments gathered from our own experience ( Phylo , DocMolecules ,
HiRE-RNA contest and Pangu) as well as examples from the growing literature on
scientific serious games
A bibliometric analysis of the Journal of Molecular Graphics and Modelling
This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported
Technological and theoretical aspects for testing electroporation on liposomes
Recently, the use of nanometer liposomes as nanocarriers in drug delivery systems mediated by nanoelectroporation has been proposed. This technique takes advantage of the possibility of simultaneously electroporating liposomes and cell membrane with 10-nanosecond pulsed electric fields (nsPEF) facilitating the release of the drug from the liposomes and at the same time its uptake by the cells. In this paper the design and characterization of a 10 nsPEF exposure system is presented, for liposomes electroporation purposes. The design and the characterization of the applicator have been carried out choosing an electroporation cuvette with 1 mm gap between the electrodes. The structure efficiency has been evaluated at different experimental conditions by changing the solution conductivity from 0.25 to 1.6 S/m. With the aim to analyze the influence of device performances on the liposomes electroporation, microdosimetric simulations have been performed considering liposomes of 200 and 400 nm of dimension with different inner and outer conductivity (from 0.05 to 1.6 S/m) in order to identify the voltage needed for their poration
Mathematics at the eve of a historic transition in biology
A century ago physicists and mathematicians worked in tandem and established
quantum mechanism. Indeed, algebras, partial differential equations, group
theory, and functional analysis underpin the foundation of quantum mechanism.
Currently, biology is undergoing a historic transition from qualitative,
phenomenological and descriptive to quantitative, analytical and predictive.
Mathematics, again, becomes a driving force behind this new transition in
biology.Comment: 5 pages, 2 figure
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