Monastyrskyy B.,University of California at Davis |
Kryshtafovych A.,University of California at Davis |
Moult J.,University of Maryland Biotechnology Institute |
Tramontano A.,University of Rome La Sapienza |
Fidelis K.,University of California at Davis
Proteins: Structure, Function and Bioinformatics | Year: 2014
The article presents the assessment of disorder region predictions submitted to CASP10. The evaluation is based on the three measures tested in previous CASPs: (i) balanced accuracy, (ii) the Matthews correlation coefficient for the binary predictions, and (iii) the area under the curve in the receiver operating characteristic (ROC) analysis of predictions using probability annotation. We also performed new analyses such as comparison of the submitted predictions with those obtained with a Naïve disorder prediction method and with predictions from the disorder prediction databases D2P2 and MobiDB. On average, the methods participating in CASP10 demonstrated slightly better performance than those in CASP9. © 2013 Wiley Periodicals, Inc.
Monastyrskyy B.,University of California at Davis |
Fidelis K.,University of California at Davis |
Moult J.,University of Maryland Biotechnology Institute |
Tramontano A.,University of Rome La Sapienza |
Kryshtafovych A.,University of California at Davis
Proteins: Structure, Function and Bioinformatics | Year: 2011
Lack of stable three-dimensional structure, or intrinsic disorder, is a common phenomenon in proteins. Naturally, unstructured regions are proven to be essential for carrying function by many proteins, and therefore identification of such regions is an important issue. CASP has been assessing the state of the art in predicting disorder regions from amino acid sequence since 2002. Here, we present the results of the evaluation of the disorder predictions submitted to CASP9. The assessment is based on the evaluation measures and procedures used in previous CASPs. The balanced accuracy and the Matthews correlation coefficient were chosen as basic measures for evaluating the correctness of binary classifications. The area under the receiver operating characteristic curve was the measure of choice for evaluating probability-based predictions of disorder. The CASP9 methods are shown to perform slightly better than the CASP7 methods but not better than the methods in CASP8. It was also shown that capability of most CASP9 methods to predict disorder decreases with increasing minimum disorder segment length. © 2011 Wiley-Liss, Inc.
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: HEALTH-2007-2.1.2-6 | Award Amount: 1.75M | Year: 2009
The aim of the PSIMEx proposal is to systematically make published molecular interaction data computationally accessible. We plan to further develop the existing standard for molecular interactions developed by the HUPO Proteomics Standards Initiative, and to promote its implementation in the entire chain from experiment planning via data formatting and analysis to data representation in journal publications and public databases. Key aspects will be the dissemination of and user training on minimum requirements for publication of molecular interaction data; the further development of the PSI-MI standard for representation of data fulfilling these minimal requirements; the specification of efficient data deposition tools and data flow from data producers to public repositories as part of the publication process; implementation of international data exchange among databases; training and exchange of curation staff in the participating databases; and the definition of analysis tools for the efficient use of data following the PSI-MI standards.
News Article | November 23, 2016
SANTA FE, NM, November 23, 2016-- Diana MacArthur has been included in Marquis Who's Who. As in all Marquis Who's Who biographical volumes, individuals profiled are selected on the basis of current reference value. Factors such as position, noteworthy accomplishments, visibility, and prominence in a field are all taken into account during the selection process.Mrs. MacArthur's professional and volunteer lives have, over the years, taken parallel paths, each reinforcing the other. She was Co-founder, Chair, and CEO of Dynamac International Inc.; CEO, Research Analysis and Management Corp.; President, Consumer Dynamics, Inc.; Program Manager, Space Division, General Electric; Vice President, Thomas J. Deegan Co. (a public relations firm in the InterPublic group); and Director, Office of Private and International Organizations, the Peace Corps. She has served as a consultant to Westinghouse, Eastman Kodak, Lever Brothers, the Hearst Corporation, the National Youth Conference on Natural Beauty and Conservation, and the National Recreation and Park Association.Complementing her professional accomplishments, Mrs. MacArthur was a member of or served on the boards of various organizations in the realms of public policy, science, education, and business. These include the following: President's Committee of Advisors on Science and Technology; Citizen's Advisory Board, President's Council on Youth Opportunity; Center for Strategic and International Studies; University of Maryland Biotechnology Institute; Smithsonian Environmental Research Center; Chancellor's Advisory Council, University System of Maryland; Tech Council of Maryland; Council on Competitiveness; Business-Higher Education Forum; Atlantic Council; Santa Fe Institute; Los Alamos National Laboratory Foundation; Science and Technology Corp., University of New Mexico; Lady Bird Johnson Wildflower Center; Menninger-Baylor College of Medicine-The Methodist Hospital Foundation; Business Advisory Committee, Center for China-U.S. Cooperation, University of Denver Graduate School of International Studies.Now retired and drawing on her wealth of experience, Mrs. MacArthur has embarked on a project in one of the most beautiful and daunting regions of the world, the Karakoram Mountains of Pakistan. On a visit to the village of MurtazaAbad, she was asked for help in constructing a building for the local school, and she agreed because her daughter had taught there. Mrs. MacArthur is now undertaking a remarkable effort to build a Center for Educational Excellence along the newly developed China-Pakistan Economic Corridor, bringing modernity to a small but economically and strategically important area of the world.She serves as the principal donor and volunteer project director of the Center, working with the local community and its representative, the Al-Murtaza Educational and Social Welfare Organization. The Center's co-ed primary/secondary schools, now under construction, will be housed in a state-of-the art, earthquake-resistant, high-tech school building, and will provide low-cost education, without discrimination based on religion, gender, ethnicity, or social status. Because a school is more than a building, the outstanding educational precepts of the Aga Khan Educational Network are being followed, and emphasis is being placed on teacher training, curriculum development, parental involvement, and efficient management and administration. Working closely with local families, Mrs. MacArthur has successfully encouraged the bringing together of the Ismaili, Shia, and Sunni Muslim communities, with the goal of providing an outstanding education to the children of the region and creating a vital civil society. Mrs. MacArthur's contributions, in time, expertise, and funding, demonstrate just how much she cares about the world and its citizens, especially children.Mrs. MacArthur has been recognized through features in Who's Who in Finance and Business, Who's Who in Science and Engineering, Who's Who of American Women, Who's Who in the East, Who's Who in the West, Who's Who in America, and Who's Who in the World.About Marquis Who's Who :Since 1899, when A. N. Marquis printed the First Edition of Who's Who in America , Marquis Who's Who has chronicled the lives of the most accomplished individuals and innovators from every significant field of endeavor, including politics, business, medicine, law, education, art, religion and entertainment. Today, Who's Who in America remains an essential biographical source for thousands of researchers, journalists, librarians and executive search firms around the world. Marquis now publishes many Who's Who titles, including Who's Who in America , Who's Who in the World , Who's Who in American Law , Who's Who in Medicine and Healthcare , Who's Who in Science and Engineering , and Who's Who in Asia . Marquis publications may be visited at the official Marquis Who's Who website at www.marquiswhoswho.com
Vagin A.,University of York |
Teplyakov A.,University of Maryland Biotechnology Institute |
Teplyakov A.,Centocor R and D Inc.
Acta Crystallographica Section D: Biological Crystallography | Year: 2010
MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and data preparation. Since the first publication describing the program, MOLREP has acquired a variety of features that include weighting of the X-ray data and search models, multi-copy search, fitting the model into electron density, structural superposition of two models and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the input data. © 2010 International Union of Crystallography Printed in Singapore - all rights reserved.
Moghaddam S.,University of Maryland Biotechnology Institute |
Yang C.,Osaka University |
Rekharsky M.,Osaka University |
Ko Y.H.,Pohang University of Science and Technology |
And 3 more authors.
Journal of the American Chemical Society | Year: 2011
A dicationic ferrocene derivative has previously been shown to bind cucurbituril (CB) in water with ultrahigh affinity (ΔGo= -21 kcal/mol). Here, we describe new compounds that bind aqueous CB equally well, validating our prior suggestion that they, too, would be ultrahigh affinity CB guests. The present guests, which are based upon either a bicyclo[2.2.2]octane or adamantane core, have no metal atoms, so these results also confirm that the remarkably high affinities of the ferrocene-based guest need not be attributed to metal-specific interactions. Because we used the M2 method to compute the affinities of several of the new host-guest systems prior to synthesizing them, the present results also provide for the first blinded evaluation of this computational method. The blinded calculations agree reasonably well with experiment and successfully reproduce the observation that the new adamantane-based guests achieve extremely high affinities, despite the fact that they position a cationic substituent at only one electronegative portal of the CB host. However, there are also significant deviations from experiment, and these lead to the correction of a procedural error and an instructive evaluation of the sensitivity of the calculations to physically reasonable variations in molecular energy parameters. The new experimental and computational results presented here bear on the physical mechanisms of molecular recognition, the accuracy of the M2 method, and the usefulness of host-guest systems as test-beds for computational methods. © 2011 American Chemical Society.
Hnizdo V.,U.S. National Institute for Occupational Safety and Health |
Gilson M.K.,University of Maryland Biotechnology Institute
Entropy | Year: 2010
The differential Shannon entropy of information theory can change under a change of variables (coordinates), but the thermodynamic entropy of a physical system must be invariant under such a change. This difference is puzzling, because the Shannon and Gibbs entropies have the same functional form. We show that a canonical change of variables can, indeed, alter the spatial component of the thermodynamic entropy just as it alters the differential Shannon entropy. However, there is also a momentum part of the entropy, which turns out to undergo an equal and opposite change when the coordinates are transformed, so that the total thermodynamic entropy remains invariant. We furthermore show how one may correctly write the change in total entropy for an isothermal physical process in any set of spatial coordinates. © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.
University of Maryland Baltimore County and University Of Maryland Biotechnology Institute | Date: 2011-10-05
The invention bioprocessing system and technique relies on non-invasive optical chemical sensing technology wherein an optical excitation source excites an optical chemical sensor. The optical chemical sensor then emits luminescence or absorbs light which is measured by a detector. The luminescence emitted from the chemical sensor or the amount of light absorbed by the chemical sensor is related to the concentration of an analyte, such as oxygen. If the luminescence emitted changes, or if the amount of light absorbed changes, then the concentration of the analyte has changed. Using such a system to measure and adjust multiple parameters at one time allows one to efficiently and cost-effectively determine optimal conditions for a given cell type and/or cell environment. By combining cell cultivation with optical chemical sensing technology, cultivation can be successfully and rapidly performed, controlled and monitored in small volumes in an automated, parallel fashion at less expense than current bioprocess techniques. Figure (1) is a schematic diagram of a high throughput microbioprocessing system in accordance with one embodiment of the present invention.
Gilson M.K.,University of Maryland Biotechnology Institute |
Gilson M.K.,La jolla Pharmaceutical
Journal of Chemical Theory and Computation | Year: 2010
Changes in mechanical stresses in a tight-binding host-guest system were computed and visualized as the cation was computationally pulled out of the cucurbituril host in a series of steps. A sharp conformational transition was observed as one of the guests ammonium groups jumped through the center of the host to the opposite portal. The conformation immediately prior to this transition was found to possess high levels of Lennard-Jones and electrostatic stress. This observation, along with the specific distribution of Lennard-Jones stress around the portals, suggested that the conformational transition resulted from steric constriction, which had been expected, and electrostatics, which was not expected. An important role for electrostatics, at least at the level of these calculations, was confirmed by a comparative computational pulling study of another guest molecule lacking the critical ammonium group. These calculations suggest that the binding kinetics of diammonium guests that position an ammonium at each cucurbituril portal will be found to be slower than the kinetics of monoammonium guests. More generally, the results suggest that computational stress analysis can provide mechanistic insight into supramolecular systems. It will be of considerable interest to extend such applications to biomolecules, for which the mechanisms of conformational change are of great scientific and practical interest. Copyright © 2010 American Chemical Society.
University Of Maryland Biotechnology Institute | Date: 2011-06-08
The present invention relates to co-expression DNA vaccines and methods for vaccinating animals against viral, bacterial and parasitic pathogens. In particular, the present invention relates to DNA vaccines that co-express antigens in combination with biologically-active components, such as adjuvants, immunoregulatory agents, antisense RNAs, and/or catalytic RNAs.