Scoring predictive models using a reduced representation of proteins: model and energy definition

January 2007
BMC Structural Biology;2007, Vol. 7, p15
Academic Journal
No abstract available.


Related Articles

  • Hierarchical modeling of protein interactions. Mateusz Kurcinski; Andrzej Kolinski // Journal of Molecular Modeling;Jul2007, Vol. 13 Issue 6/7, p691 

    Abstract  A novel approach to hierarchical peptide–protein and protein–protein docking is described and evaluated. Modeling procedure starts from a reduced space representation of proteins and peptides. Polypeptide chains are represented by strings of alpha-carbon beads...

  • Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes. Beard, Hege; Cholleti, Anuradha; Pearlman, David; Sherman, Woody; Loving, Kathryn A. // PLoS ONE;Dec2013, Vol. 8 Issue 12, p1 

    Predicting changes in protein binding affinity due to single amino acid mutations helps us better understand the driving forces underlying protein-protein interactions and design improved biotherapeutics. Here, we use the MM-GBSA approach with the OPLS2005 force field and the VSGB2.0 solvent...

  • Protein structure validation using a semi-empirical method. Lahiri, Tapobrata; Singh, Kalpana; Pal, Manoj Kumar; Verma, Gaurav // Bioinformation;2012, Vol. 8 Issue 20, p984 

    Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage...

  • NCACO-score: An effective main-chain dependent scoring function for structure modeling. Liqing Tian; Aiping Wu; Yang Cao; Xiaoxi Dong; Yun Hu; Taijiao Jiang // BMC Bioinformatics;2011, Vol. 12 Issue 1, p208 

    Background: Development of effective scoring functions is a critical component to the success of protein structure modeling. Previously, many efforts have been dedicated to the development of scoring functions. Despite these efforts, development of an effective scoring function that can achieve...

  • A comparison of different functions for predicted protein model quality assessment. Li, Juan; Fang, Huisheng // Journal of Computer-Aided Molecular Design;Jul2016, Vol. 30 Issue 7, p553 

    In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template...

  • PREDICTIVE MODEL.  // Encyclopedia of Operations Research & Management Science;2001, p631 

    A definition of the term "predictive model" is presented. It refers to the model used to predict the future course of events and as an aid to decision making.

  • Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions. Elkin, Michael; Andre, Ingemar; Lukatsky, David // Journal of Statistical Physics;Feb2012, Vol. 146 Issue 4, p870 

    Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of protein-protein, protein-DNA, and protein-RNA binding....

  • Some notes on internal and external relations and representation. Bickhard, Mark H. // Consciousness & Emotion;2003, Vol. 4 Issue 1, p101 

    Presents insights on internal and external relations and representation. Definitions of internal relations and representation; Interactive model of representation; Part models of representation; Description of the interactive model.

  • Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique. Wei, Guanghong; Mousseau, Normand; Derreumaux, Philippe // Journal of Chemical Physics;12/22/2002, Vol. 117 Issue 24, p11379 

    Finding the global energy minimum region of a polypeptide chain, independently of the starting conformation and in a reasonable computational time, is of fundamental interest. As the energy landscape of proteins is very rugged, sampling is hindered by the vast number of minima existing on this...

  • Critically assessing the state-of-the-art in protein structure prediction. Jones, D. T. // Pharmacogenomics Journal;2001, Vol. 1 Issue 2, p126 

    Discusses the prediction of the structure of proteins. Use of comparative modeling in predicting the three-dimensional structure of proteins; Application of protein fold recognition methods in predicting protein structure; Details on automated protein structure prediction.


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics