Literature DB >> 19217386

Outcome of a workshop on applications of protein models in biomedical research.

Torsten Schwede1, Andrej Sali, Barry Honig, Michael Levitt, Helen M Berman, David Jones, Steven E Brenner, Stephen K Burley, Rhiju Das, Nikolay V Dokholyan, Roland L Dunbrack, Krzysztof Fidelis, Andras Fiser, Adam Godzik, Yuanpeng Janet Huang, Christine Humblet, Matthew P Jacobson, Andrzej Joachimiak, Stanley R Krystek, Tanja Kortemme, Andriy Kryshtafovych, Gaetano T Montelione, John Moult, Diana Murray, Roberto Sanchez, Tobin R Sosnick, Daron M Standley, Terry Stouch, Sandor Vajda, Max Vasquez, John D Westbrook, Ian A Wilson.   

Abstract

We describe the proceedings and conclusions from the "Workshop on Applications of Protein Models in Biomedical Research" (the Workshop) that was held at the University of California, San Francisco on 11 and 12 July, 2008. At the Workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) the requirements and challenges for different applications, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.

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Year:  2009        PMID: 19217386      PMCID: PMC2739730          DOI: 10.1016/j.str.2008.12.014

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  97 in total

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2.  Protein structure determination from NMR chemical shifts.

Authors:  Andrea Cavalli; Xavier Salvatella; Christopher M Dobson; Michele Vendruscolo
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3.  Identification of a chloride ion binding site in Na+/Cl -dependent transporters.

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Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-24       Impact factor: 11.205

4.  Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data.

Authors:  J K Amisha Kamal; Sabrina A Benchaar; Keiji Takamoto; Emil Reisler; Mark R Chance
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5.  Novel leverage of structural genomics.

Authors:  Jinfeng Liu; Gaetano T Montelione; Burkhard Rost
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

Review 6.  Drug evaluation: PRX-00023, a selective 5-HT1A receptor agonist for depression.

Authors:  Tomas de Paulis
Journal:  Curr Opin Investig Drugs       Date:  2007-01

7.  Characterizing the 1,4-dihydropyridines binding interactions in the L-type Ca2+ channel: model construction and docking calculations.

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Journal:  Nat Genet       Date:  2007-05-07       Impact factor: 38.330

9.  Prediction and assignment of function for a divergent N-succinyl amino acid racemase.

Authors:  Ling Song; Chakrapani Kalyanaraman; Alexander A Fedorov; Elena V Fedorov; Margaret E Glasner; Shoshana Brown; Heidi J Imker; Patricia C Babbitt; Steven C Almo; Matthew P Jacobson; John A Gerlt
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10.  Functional impact of missense variants in BRCA1 predicted by supervised learning.

Authors:  Rachel Karchin; Alvaro N A Monteiro; Sean V Tavtigian; Marcelo A Carvalho; Andrej Sali
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  69 in total

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Authors:  Ryan Day; Xiaotao Qu; Rosemarie Swanson; Zach Bohannan; Robert Bliss; Jerry Tsai
Journal:  J Comput Biol       Date:  2011-01       Impact factor: 1.479

2.  Engineering encodable lanthanide-binding tags into loop regions of proteins.

Authors:  Katja Barthelmes; Anne M Reynolds; Ezra Peisach; Hendrik R A Jonker; Nicholas J DeNunzio; Karen N Allen; Barbara Imperiali; Harald Schwalbe
Journal:  J Am Chem Soc       Date:  2011-02-02       Impact factor: 15.419

Review 3.  Biomolecularmodeling and simulation: a field coming of age.

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Journal:  Q Rev Biophys       Date:  2011-05       Impact factor: 5.318

Review 4.  Advances in protein NMR provided by the NIGMS Protein Structure Initiative: impact on drug discovery.

Authors:  Gaetano T Montelione; Thomas Szyperski
Journal:  Curr Opin Drug Discov Devel       Date:  2010-05

5.  The ClusPro web server for protein-protein docking.

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Review 6.  Structure-based inhibition of protein-protein interactions.

Authors:  Andrew M Watkins; Paramjit S Arora
Journal:  Eur J Med Chem       Date:  2014-09-16       Impact factor: 6.514

7.  Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing.

Authors:  Jacqueline Morris; Young-Ji Na; Hua Zhu; Jae-Hee Lee; Hoa Giang; Alexandra V Ulyanova; Gordon H Baltuch; Steven Brem; H Isaac Chen; David K Kung; Timothy H Lucas; Donald M O'Rourke; John A Wolf; M Sean Grady; Jai-Yoon Sul; Junhyong Kim; James Eberwine
Journal:  Cell Rep       Date:  2017-12-05       Impact factor: 9.423

8.  Assessment of template-based protein structure predictions in CASP10.

Authors:  Yuanpeng J Huang; Binchen Mao; James M Aramini; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

Review 9.  Modelling three-dimensional protein structures for applications in drug design.

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Journal:  Drug Discov Today       Date:  2013-11-08       Impact factor: 7.851

10.  SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.

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Journal:  PLoS Comput Biol       Date:  2010-01-22       Impact factor: 4.475

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