Andras Fiser

..For a rapid response, ModLoop runs on a cluster of Linux PC computers. AVAILABILITY: The server is freely accessible to academic users at http://salilab.org/modloop..

..The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques...

..An essential step towards understanding molecular mechanisms controlling transitions between the various life stages and identifying candidate drug targets is to accurately characterize the T. gondii proteome...

..Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo...

..gondii or to the Apicomplexa, providing a set of gene predictions ripe for experimental investigation, and potentially suitable targets for the development of therapeutic strategies...

..Methylation, a PTM not previously described on tubulin, was also detected. Methylated tubulins were not detected in the host cells, human foreskin fibroblasts, suggesting that this may be a modification specific to the Apicomplexa...

..High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data...

..The performance of M4T has been benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set, and showed favorable performance to current state of the art methods...

..The functional role of residues around Gly-189 and Gly-192 is consistent with a molecular structural model in which these two residues along with Ieu-188 are accessible to the PCFT aqueous translocation pathway...

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..The performance of M4T was benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set and showed a favorable performance to current state-of-the-art methods...

..The data illustrate how alterations in carrier cycling can impact influx K(t) without comparable alterations in substrate binding to the carrier...

..These technical improvements allow this method to be used for investigating protein-protein interactions in complex biological samples...

..The accuracy of the scoring function was further increased by using BLOSUM mutation table scores...

..Hence, despite its location, the P425R-PCFT mutation produces a conformational change that fully preserves pemetrexed binding but markedly impairs binding of methotrexate and other folates to the carrier...

..The applicability and performance of these approaches depend on the availability of short fragments in structure databanks...

..These findings suggest that V region conformational changes can be dictated by the C(H) domains through an allosteric effect involving networks of highly connected amino acids...

..This demonstrates the feasibility of analyzing cellular compartment-specific proteins in archived tissue samples with the simple DDF method...

..Hence, D156 plays a critical role in PCFT protein stability, and D109, located in the first intracellular loop between the second and third transmembrane domains, is absolutely required for PCFT function...

..These features may make the method suitable to investigate protein-protein interactions in biological samples...

..A new definition for reference state, free of the observed systematic errors, is suggested. It has been demonstrated to generate statistical potentials that compare favorably to other publicly available ones...

..Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment...

..Strategies for template-based structure modeling will be discussed with a focus on comparative modeling, by reviewing techniques available for all the major steps involved in the comparative modeling pipeline...

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..The method we developed predicts disulfide bond connectivity patterns with accuracies of 73, 69 and 61% for proteins with two, three and four disulfide bonds, respectively...

..The His281 residue is not essential for proton coupling but plays an important role in PCFT protonation, which, in turn, augments folate binding to the carrier...

..These results identify the first linear neutralizing epitopes of PA and show that peptides containing epitope sequences can elicit neutralizing antibody responses, a finding that could be exploited for vaccine design...

..The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model. AVAILABILITY: The MMM server is freely accessible at http://www.fiserlab.org/servers/mmm..

..To understand these surprising observations a 3D-model of MurM was constructed, which helped to put into structural context several of the biochemical and genetic observations made about this protein...

..MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable similarity in size, shape, and electrostatics to DNA...

..The present study also opens avenues for locating drug and protein binding sites and for deciphering the mechanisms by which their interactions alter the conformation of microtubules and tubulin dimers...

..This study shows that the enhanced transforming potential of p110β is the result of its decreased inhibition by p85, due to the disruption of an inhibitory C2-iSH2 domain interface...

..Pinpointing impaired interaction between NAP57 and SHQ1 as a potential molecular basis for X-linked DC has implications for therapeutic approaches, e.g. by targeting the NAP57-SHQ1 interface with small molecules...

..This projected resource will provide structural biology information important to understanding the function of most proteins of the cell...

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..Web-based resources, such as EPIC-DB and ToxoDB, provide proteomic data and support for studies on T. gondii. This review will summarize the current status of proteomic research on T. gondii...

..47 A of r.m.s.d. accuracy, respectively. In a head to head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method...

..MMM also compared favorably over two alignment meta-servers. The algorithm is computationally efficient; therefore, it is a suitable tool for genome scale modeling studies...

..47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method...

..Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation...

..Meanwhile, in highly interconnected architectures (represented by long promoters), robustness evolves almost entirely via network level changes, deleting and creating binding sites that modify the network architecture...

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..Furthermore, isotype affected the polyreactivity of V region identical antibodies, implying a role for C region in determining self-reactivity...

..parapsilosis in complex with ASA. The results suggest that development of inhibitors of fungal lipases could result in broad-spectrum therapeutics, especially since fungal lipases are not homologous to their human analogues...

..Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed...