%0 Journal Article %1 ISI:000237863100023 %A Yun, MR %A Lavery, R %A Mousseau, N %A Zakrzewska, K %A Derreumaux, P %C DIV JOHN WILEY & SONS INC, 111 RIVER ST, HOBOKEN, NJ 07030 USA %D 2006 %I WILEY-LISS %J PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS %K ACTIVATION METHOD energy landscape sampling %N 4 %P 967-975 %R 10.1002/prot.20938 %T ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes %V 63 %X We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate. space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational. changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly. Proteins 2006;63:967-975. (c) 2006 Wiley-Liss, Inc.

@article{ISI:000237863100023, abstract = {{We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate. space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational. changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly. Proteins 2006;63:967-975. (c) 2006 Wiley-Liss, Inc.}}, added-at = {2009-01-05T01:47:42.000+0100}, address = {{DIV JOHN WILEY \& SONS INC, 111 RIVER ST, HOBOKEN, NJ 07030 USA}}, affiliation = {{Derreumaux, P (Reprint Author), CNRS, Lab Biochim Theor, UPR 9080, Inst Biol Physicochim, 13 Rue Pierre \& Marie Curie, F-75005 Paris, France. CNRS, Lab Biochim Theor, UPR 9080, Inst Biol Physicochim, F-75005 Paris, France. Univ Paris, F-75252 Paris, France. Univ Montreal, Dept Phys, Montreal, PQ H3C 3J7, Canada. Univ Montreal, Ctr Bioinformat Robert Cedergren, Montreal, PQ, Canada.}}, author = {Yun, MR and Lavery, R and Mousseau, N and Zakrzewska, K and Derreumaux, P}, author-email = {{philippe.derreumaux@ibpc.fr}}, biburl = {https://www.bibsonomy.org/bibtex/2338fda457fe1add73381492d130c7a2e/huiyangsfsu}, cited-references = {{ABAGYAN R, 1994, J MOL BIOL, V235, P983. BARKEMA GT, 1996, PHYS REV LETT, V77, P4358. BASTARD K, 2003, J COMPUT CHEM, V24, P1910, DOI 10.1002/JCC.10329. 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TJERNBERG L, 2002, J BIOL CHEM, V277, P43243, DOI 10.1074/jbc.M205570200. TSUI V, 2000, BIOPOLYMERS, V56, P275. WEI GH, 2002, J CHEM PHYS, V117, P11379, DOI 10.1063/1.1522373. WEI GH, 2004, BIOPHYS J, V87, P3648, DOI 10.1529/biophysj.104.047688.}}, doc-delivery-number = {{047ER}}, doi = {{10.1002/prot.20938}}, interhash = {633a10618ec399d7a07cc010343978ef}, intrahash = {338fda457fe1add73381492d130c7a2e}, issn = {{0887-3585}}, journal = {{PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}}, journal-iso = {{Proteins}}, keywords = {ACTIVATION METHOD energy landscape sampling}, keywords-plus = {{MONTE-CARLO SIMULATIONS; NORMAL-MODE ANALYSIS; MOLECULAR-DYNAMICS; CONFORMATIONAL TRANSITIONS; A-BETA(16-22) PEPTIDE; RELAXATION TECHNIQUE; SOLVATION MODEL; IN-SILICO; MECHANICS; SYSTEMS}}, language = {{English}}, month = {{JUN 1}}, note = {ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes (p 967-975) Mi-Ran Yun, R. Lavery, N. Mousseau, K. Zakrzewska, P. Derreumaux Published Online: Mar 7 2006 1:53PM DOI: 10.1002/prot.20938 }, number = {{4}}, number-of-cited-references = {{46}}, pages = {{967-975}}, publisher = {{WILEY-LISS}}, subject-category = {{Biochemistry \& Molecular Biology; Biophysics}}, times-cited = {{4}}, timestamp = {2009-01-05T01:47:42.000+0100}, title = {{ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes}}, type = {{Article}}, unique-id = {{ISI:000237863100023}}, volume = {{63}}, year = {{2006}} }