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Predicted Interaction (predicted + interaction)

Distribution by Scientific Domains

Chemistry	60%

Selected Abstracts

Assessing predictions of protein,protein interaction: The CAPRI experiment

PROTEIN SCIENCE, Issue 2 2005
Joël Janin
Abstract The Critical Assessment of PRedicted Interactions (CAPRI) experiment was designed in 2000 to test protein docking algorithms in blind predictions of the structure of protein,protein complexes. In four years, 17 complexes offered by crystallographers as targets prior to publication, have been subjected to structure prediction by docking their two components. Models of these complexes were submitted by predictor groups and assessed by comparing their geometry to the X-ray structure and by evaluating the quality of the prediction of the regions of interaction and of the pair wise residue contacts. Prediction was successful on 12 of the 17 targets, most of the failures being due to large conformation changes that the algorithms could not cope with. Progress in the prediction quality observed in four years indicates that the experiment is a powerful incentive to develop new procedures that allow for flexibility during docking and incorporate nonstructural information. We therefore call upon structural biologists who study protein,protein complexes to provide targets for further rounds of CAPRI predictions. [source]

Flexible protein-protein docking based on Best-First search algorithm

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010
Efrat Noy
Abstract We developed a new high resolution protein-protein docking method based on Best-First search algorithm that loosely imitates protein-protein associations. The method operates in two stages: first, we perform a rigid search on the unbound proteins. Second, we search alternately on rigid and flexible degrees of freedom starting from multiple configurations from the rigid search. Both stages use heuristics added to the energy function, which causes the proteins to rapidly approach each other and remain adjacent, while optimizing on the energy. The method deals with backbone flexibility explicitly by searching over ensembles of conformations generated before docking. We ran the rigid docking stage on 66 complexes and grouped the results into four classes according to evaluation criteria used in Critical Assessment of Predicted Interactions (CAPRI; "high," "medium," "acceptable," and "incorrect"). Our method found medium binding conformations for 26% of the complexes and acceptable for additional 44% among the top 10 configurations. Considering all the configurations, we found medium binding conformations for 55% of the complexes and acceptable for additional 39% of the complexes. Introducing side-chains flexibility in the second stage improves the best found binding conformation but harms the ranking. However, introducing side-chains and backbone flexibility improve both the best found binding conformation and the best found conformation in the top 10. Our approach is a basis for incorporating multiple flexible motions into protein-protein docking and is of interest even with the current use of a simple energy function. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

Persuasive constraint and expert versus non-expert influence in intention to quit smoking

EUROPEAN JOURNAL OF SOCIAL PSYCHOLOGY, Issue 2 2002
Juan Manuel Falomir-Pichastor
In a 2,×,2 design, after listing important personal reasons for smoking, 70 smokers were randomly told either that they had sufficient reasons for smoking (low internal constraint to change) or that they did not have sufficient reasons (high internal constraint to change) and were exposed to an anti-smoking message from a source with either expert (high external constraint to change) or non-expert (low external constraint to change) status. The main dependent variable was change in intention to give up smoking. The analyses revealed the predicted interaction between external and internal constraint: High internal constraint increased non-expert influence but not expert influence. Supplementary analysis showed that, when internal constraint was high, non-expert influence was related to the perceived quality of the message whereas when internal constraint was low, expert influence was related to the source's perceived motivation to inform, i.e. rather than to convince. These results were predicted on the basis of the link that targets establish in social influence settings between constraints to change that are internal (i.e. related to their personal beliefs, feelings or attitudes) and those that are external (i.e. related to the characteristics of the persuasive communication such as the status of the source). Copyright © 2002 John Wiley & Sons, Ltd. [source]

Political Conservatism, Need for Cognitive Closure, and Intergroup Hostility

POLITICAL PSYCHOLOGY, Issue 4 2010
Agnieszka Golec De Zavala
Two studies examined the interaction of political conservatism and the need for cognitive closure in predicting aggressiveness in intergroup conflict and hostility toward outgroups. In the first study, Polish participants indicated their preference for coercive conflict strategies in the context of a real-life intergroup conflict. Only among participants who identify themselves as conservative, need for cognitive closure was positively and significantly related to preference for aggressive actions against the outgroup. In the second study, the predicted interaction was investigated in the context of the terrorist threat in Poland. The findings indicated that high in need for closure conservatives showed greater hostility against Arabs and Muslims only when they believed that Poland was under threat of terrorist attacks inspired by Islamist fundamentalism. [source]

Macromolecular recognition in the Protein Data Bank

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2007
Joël Janin
Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein,protein and protein,DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200,2000,Å2 of protein surface occur in protease,inhibitor and antigen,antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes. [source]