1 resultado para Local-regional space
em Boston University Digital Common
Filtro por publicador
- Repository Napier (1)
- Aberystwyth University Repository - Reino Unido (2)
- Academic Archive On-line (Jönköping University; Sweden) (1)
- Academic Archive On-line (Stockholm University; Sweden) (1)
- Academic Research Repository at Institute of Developing Economies (1)
- Acceda, el repositorio institucional de la Universidad de Las Palmas de Gran Canaria. España (2)
- AMS Tesi di Dottorato - Alm@DL - Università di Bologna (1)
- Andina Digital - Repositorio UASB-Digital - Universidade Andina Simón Bolívar (8)
- Aquatic Commons (79)
- ArchiMeD - Elektronische Publikationen der Universität Mainz - Alemanha (2)
- Archive of European Integration (6)
- Archivo Digital para la Docencia y la Investigación - Repositorio Institucional de la Universidad del País Vasco (2)
- Aston University Research Archive (7)
- Avian Conservation and Ecology - Eletronic Cientific Hournal - Écologie et conservation des oiseaux: (2)
- Biblioteca Digital | Sistema Integrado de Documentación | UNCuyo - UNCUYO. UNIVERSIDAD NACIONAL DE CUYO. (2)
- Biblioteca Digital da Produção Intelectual da Universidade de São Paulo (5)
- Biblioteca Digital da Produção Intelectual da Universidade de São Paulo (BDPI/USP) (9)
- Biblioteca Digital de Artesanías de Colombia (3)
- Biblioteca Digital de la Universidad Católica Argentina (1)
- Biblioteca Digital de Teses e Dissertações Eletrônicas da UERJ (12)
- Bioline International (1)
- BORIS: Bern Open Repository and Information System - Berna - Suiça (27)
- Boston University Digital Common (1)
- Brock University, Canada (4)
- Bucknell University Digital Commons - Pensilvania - USA (5)
- Bulgarian Digital Mathematics Library at IMI-BAS (1)
- CaltechTHESIS (4)
- Cambridge University Engineering Department Publications Database (3)
- CentAUR: Central Archive University of Reading - UK (55)
- Chinese Academy of Sciences Institutional Repositories Grid Portal (11)
- Cochin University of Science & Technology (CUSAT), India (4)
- Comissão Econômica para a América Latina e o Caribe (CEPAL) (21)
- CORA - Cork Open Research Archive - University College Cork - Ireland (2)
- Dalarna University College Electronic Archive (3)
- Deakin Research Online - Australia (61)
- DI-fusion - The institutional repository of Université Libre de Bruxelles (3)
- Digital Archives@Colby (1)
- Digital Commons - Michigan Tech (3)
- Digital Commons @ DU | University of Denver Research (1)
- Digital Commons at Florida International University (6)
- DigitalCommons@The Texas Medical Center (1)
- Doria (National Library of Finland DSpace Services) - National Library of Finland, Finland (1)
- Duke University (6)
- Ecology and Society (1)
- eResearch Archive - Queensland Department of Agriculture; Fisheries and Forestry (3)
- FAUBA DIGITAL: Repositorio institucional científico y académico de la Facultad de Agronomia de la Universidad de Buenos Aires (3)
- Glasgow Theses Service (2)
- Greenwich Academic Literature Archive - UK (2)
- Helda - Digital Repository of University of Helsinki (8)
- Indian Institute of Science - Bangalore - Índia (20)
- Instituto Nacional de Saúde de Portugal (1)
- Massachusetts Institute of Technology (1)
- Memoria Académica - FaHCE, UNLP - Argentina (23)
- Ministerio de Cultura, Spain (29)
- Plymouth Marine Science Electronic Archive (PlyMSEA) (14)
- Portal de Revistas Científicas Complutenses - Espanha (3)
- Publishing Network for Geoscientific & Environmental Data (4)
- QSpace: Queen's University - Canada (1)
- QUB Research Portal - Research Directory and Institutional Repository for Queen's University Belfast (61)
- Queensland University of Technology - ePrints Archive (145)
- RCAAP - Repositório Científico de Acesso Aberto de Portugal (1)
- RDBU - Repositório Digital da Biblioteca da Unisinos (1)
- ReCiL - Repositório Científico Lusófona - Grupo Lusófona, Portugal (5)
- Repositório Aberto da Universidade Aberta de Portugal (1)
- Repositorio Académico de la Universidad Nacional de Costa Rica (9)
- Repositório Alice (Acesso Livre à Informação Científica da Embrapa / Repository Open Access to Scientific Information from Embrapa) (1)
- Repositório Científico da Universidade de Évora - Portugal (3)
- Repositório Científico do Instituto Politécnico de Lisboa - Portugal (2)
- Repositório Científico do Instituto Politécnico de Santarém - Portugal (1)
- Repositório digital da Fundação Getúlio Vargas - FGV (5)
- Repositório Digital da UNIVERSIDADE DA MADEIRA - Portugal (1)
- Repositório Digital da Universidade Municipal de São Caetano do Sul - USCS (3)
- Repositório Institucional da Universidade de Aveiro - Portugal (6)
- Repositório Institucional da Universidade Estadual de São Paulo - UNESP (2)
- Repositório Institucional da Universidade Federal do Rio Grande do Norte (1)
- Repositorio Institucional de la Universidad de El Salvador (1)
- Repositorio Institucional de la Universidad de Málaga (1)
- Repositorio Institucional de la Universidad Nacional Agraria (1)
- Repositório Institucional UNESP - Universidade Estadual Paulista "Julio de Mesquita Filho" (40)
- Repositorio Institucional Universidad EAFIT - Medelin - Colombia (1)
- RUN (Repositório da Universidade Nova de Lisboa) - FCT (Faculdade de Cienecias e Technologia), Universidade Nova de Lisboa (UNL), Portugal (6)
- SAPIENTIA - Universidade do Algarve - Portugal (6)
- Universidad de Alicante (3)
- Universidad del Rosario, Colombia (26)
- Universidad Politécnica de Madrid (6)
- Universidade de Lisboa - Repositório Aberto (6)
- Universidade Federal do Pará (10)
- Universidade Federal do Rio Grande do Norte (UFRN) (18)
- Universidade Metodista de São Paulo (6)
- Universitat de Girona, Spain (6)
- Universitätsbibliothek Kassel, Universität Kassel, Germany (3)
- Université de Lausanne, Switzerland (2)
- Université de Montréal (1)
- Université de Montréal, Canada (15)
- University of Connecticut - USA (1)
- University of Michigan (6)
- University of Queensland eSpace - Australia (8)
- WestminsterResearch - UK (7)
- Worcester Research and Publications - Worcester Research and Publications - UK (1)
Resumo:
Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 � ligand interface Ca root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods.