Tag post-defense [69 articles] Export

Recent papers classified by the tag post-defense.

	Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 25. (9 December 2003), pp. 14800-14805. by K. Weninger, M. E. Bowen, S. Chu, A. T. Brunger posted to antiparallel post-defense snare by kgutwin on 2009-05-22 04:13:49 as along with 1 person yusdi
	The molecular architecture of the nuclear pore complex [My Copy] Nature, Vol. 450, No. 7170. (29 November 2007), pp. 695-701. by Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, et al.Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit Karni-Schmidt, Rosemary Williams, Brian T. Chait, Andrej Sali, Michael P. Rout posted to npc post-defense structure by kgutwin on 2009-05-21 01:17:30 as along with 9 people MatthiasReimann hadesnumb chad_davis neils cjeans zwang mkikkawa faion phoenixzxl
	Integrating Diverse Data for Structure Determination of Macromolecular Assemblies [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (4 March 2008), pp. 443-477. by Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali posted to npc review post-defense by kgutwin on 2009-05-21 01:16:02 as along with 5 people mijam carlk noraziz chad_davis phoenixzxl
	A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. [My Copy] Proc Natl Acad Sci U S A, Vol. 97, No. 24. (21 November 2000), pp. 13203-13208. by J. R. Newman, E. Wolf, P. S. Kim posted to coiled-coils post-defense yeast-2-hybrid by kgutwin on 2009-05-20 23:51:30 as along with 2 people hplatero phoenixzxl
	Crystal structure of the endosomal SNARE complex reveals common structural principles of all SNAREs [My Copy] Nat Struct Mol Biol, Vol. 9, No. 2. (February 2002), pp. 107-111. by Wolfram Antonin, Dirk Fasshauer, Stefan Becker, Reinhard Jahn, Thomas R. Schneider posted to post-defense review snare structure by kgutwin on 2009-05-20 23:45:44 as
	SNAREs — engines for membrane fusion [My Copy] Nature Reviews Molecular Cell Biology, Vol. 7, No. 9. (16 August 2006), pp. 631-643. by Reinhard Jahn, Richard H. Scheller posted to post-defense review snare specificity by kgutwin on 2009-05-20 23:44:56 as along with 1 person and 1 group borisbernhardt NOEL
	The specificity of SNARE-dependent fusion is encoded in the SNARE motif. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 10. (9 March 2004), pp. 3376-3380. by F. Paumet, V. Rahimian, J. E. Rothman posted to coiled-coils post-defense snare specificity by kgutwin on 2009-05-20 23:32:19 as along with 1 person marck
	Binding interactions control SNARE specificity in vivo [My Copy] J. Cell Biol., Vol. 183, No. 6. (15 December 2008), pp. 1089-1100. by Hui-Ju Yang, Hideki Nakanishi, Song Liu, James A. Mcnew, Aaron M. Neiman posted to post-defense snare specificity by kgutwin on 2009-05-20 23:31:58 as
	The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway [My Copy] Science, Vol. 311, No. 5762. (10 February 2006), pp. 822-826. by Roby P. Bhattacharyya, Attila Remenyi, Matthew C. Good, Caleb J. Bashor, Arnold M. Falick, Wendell A. Lim posted to post-defense scaffold by kgutwin on 2009-05-20 21:03:35 as along with 3 people nirfriedman tmt laurabailey
	Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. [My Copy] Science, Vol. 299, No. 5609. (14 February 2003), pp. 1061-1064. by S. H. Park, A. Zarrinpar, W. A. Lim posted to kinase post-defense scaffold by kgutwin on 2009-05-20 21:03:08 as along with 2 people rklancer tmt
	Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics [My Copy] Science, Vol. 319, No. 5869. (14 March 2008), pp. 1539-1543. by Caleb J. Bashor, Noah C. Helman, Shude Yan, Wendell A. Lim posted to bzip kinase post-defense scaffold by kgutwin on 2009-05-20 21:02:53 as along with 6 people jsaucerman yarikson reidw lisa1 biomcgary melting
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1 May 1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted to amber post-defense potential by kgutwin on 2009-05-20 08:03:04 as along with 6 people Lombardo_7 softsimu coomteng flbarroso pavanghatty dfgreen
	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217. by Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus posted to charmm post-defense potential by kgutwin on 2009-05-20 08:02:38 as along with 16 people ubcg08l flbarroso nickolay newton1234 r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra dfgreen Lombardo_7 dgront mmuecke rabio saravan gisle
	Ab initio modeling of small proteins by iterative TASSER simulations [My Copy] BMC Biology, Vol. 5 (08 May 2007), 17. by Sitao Wu, Jeffrey Skolnick, Yang Zhang posted to ab-initio post-defense tasser by kgutwin on 2009-05-20 07:47:17 as along with 2 people saunders j3xucite
	Template-based modeling and free modeling by I-TASSER in CASP7 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 108-117. by Yang Zhang posted to casp post-defense predictions structure tasser ab-initio by kgutwin on 2009-05-20 07:39:31 as
	Physically realistic homology models built with ROSETTA can be more accurate than their templates. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5361-5366. by K. M. Misura, D. Chivian, C. A. Rohl, D. E. Kim, D. Baker posted to homology-model post-defense rosetta by kgutwin on 2009-05-20 07:38:28 as along with 6 people j3xucite jwm balajis dgront bilab BioNica
	Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. [My Copy] Proteins, Vol. 69, No. S8. (25 September 2007), pp. 118-128. by Rhiju Das, Bin Qian, Srivatsan Raman, et al.Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D D. Tyka, Divya Bhat, Dylan Chivian, David E E. Kim, William H H. Sheffler, Lars Malmström, Andrew M M. Wollacott, Chu Wang, Ingemar Andre, David Baker posted to casp post-defense predictions rosetta structure ab-initio by kgutwin on 2009-05-20 07:37:22 as along with 3 people mcbla jwm Ema
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to docking post-defense rosetta by kgutwin on 2009-05-20 07:36:57 as along with 6 people and 2 groups mijam csrocha barry jwm xdeupi Ema structural_bioinformatics Bioinformatics
	Macromolecular Modeling with Rosetta [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008), pp. 363-382. by Rhiju Das, David Baker posted to ab-initio post-defense review rosetta by kgutwin on 2009-05-20 07:36:42 as along with 9 people bmduggan choonpeng mijam carlk phoenixzxl krapnik flbarroso saunders gisle
	KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. [My Copy] Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007) by Y. H. Wong, T. Y. Lee, H. K. Liang, et al.C. M. Huang, T. Y. Wang, Y. H. Yang, C. H. Chu, H. D. Huang, M. T. Ko, J. K. Hwang posted to kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:16:33 as along with 1 person guhjy
	Kinase-specific prediction of protein phosphorylation sites. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 527 (2009) by M. L. Miller, N. Blom posted to kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:16:14 as along with 2 people niallhaslam hryk
	Substrate specificity of protein kinases and computational prediction of substrates. [My Copy] Biochim Biophys Acta, Vol. 1754, No. 1-2. (30 December 2005), pp. 200-209. by B. Kobe, T. Kampmann, J. K. Forwood, P. Listwan, R. I. Brinkworth posted to domains kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:06:52 as
	The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. [My Copy] Science, Vol. 241, No. 4861. (1 July 1988), pp. 42-52. by S. K. Hanks, A. M. Quinn, T. Hunter posted to domains kinase post-defense by kgutwin on 2009-05-20 07:01:32 as along with 2 people dragonrez jnk1
	The evolving model of calmodulin structure, function and activation. [My Copy] Structure (London, England : 1993), Vol. 3, No. 1. (15 January 1995), pp. 7-11. by B. E. Finn, S. Forsén posted to calmodulin domains ef-hand post-defense by kgutwin on 2009-05-20 07:00:49 as
	Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. [My Copy] Cell biochemistry and biophysics, Vol. 50, No. 3. (2008), pp. 111-131. by K. J. Brayer, D. J. Segal posted to interactions post-defense review zincfinger by kgutwin on 2009-05-20 06:38:19 as along with 1 person dsekaran
	Zinc fingers--folds for many occasions. [My Copy] IUBMB life, Vol. 54, No. 6. (December 2002), pp. 351-355. by J. M. Matthews, M. Sunde posted to post-defense review zincfinger by kgutwin on 2009-05-20 06:37:58 as
	Structure and dynamic regulation of Src-family kinases. [My Copy] Cellular and molecular life sciences : CMLS, Vol. 65, No. 19. (October 2008), pp. 3058-3073. by J. R. Engen, T. E. Wales, J. M. Hochrein, et al.M. A. Meyn, S. Banu Ozkan, I. Bahar, T. E. Smithgall posted to domains post-defense sh2 sh3 by kgutwin on 2009-05-20 06:09:19 as along with 1 person guhjy
	Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains [My Copy] Mol Cell Proteomics (20 November 2008), M800450-MCP200. by Tingjun Hou, Zheng Xu, Wei Zhang, et al.William A. Mclaughlin, David A. Case, Yang Xu, Wei Wang posted to domains post-defense predictions sh3 by kgutwin on 2009-05-20 05:41:36 as along with 2 people phoenixzxl zwang
	Structure Based Prediction of the S. cerevisiae SH3-Ligand Interactions. [My Copy] Journal of molecular biology (23 March 2009) by Gregorio Fernandez-Ballester, Pedro Beltrao, Jose Manuel M. Gonzalez, et al.Young-Hwa H. Song, Matthias Wilmanns, Alfonso Valencia, Luis Serrano posted to domains ism post-defense predictions sh3 by kgutwin on 2009-05-20 05:41:04 as along with 1 person neils
	Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. [My Copy] Nucleic acids research, Vol. 36, No. 10. (June 2008), pp. 3263-3273. by L. Li, C. Wu, H. Huang, K. Zhang, J. Gan, S. S. Li posted to domains post-defense predictions sh2 by kgutwin on 2009-05-20 05:40:08 as along with 1 person hryk
	A Specificity Map for the PDZ Domain Family [My Copy] PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239. by Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, et al.Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A. Held, Brent A. Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C. Chan, Somasekar Seshagiri, Laurence A. Lasky, Chris Sander, Charles Boone, Gary D. Bader, Sachdev S. Sidhu posted to domains pdz post-defense predictions by kgutwin on 2009-05-20 05:37:28 as along with 6 people and 3 groups balicea grahamc markchen zwang cabbagesofdoom barry structural_bioinformatics McCammon Bioinformatics
	Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. [My Copy] Journal of molecular biology, Vol. 343, No. 3. (22 October 2004), pp. 703-718. by U. Wiedemann, P. Boisguerin, R. Leben, et al.D. Leitner, G. Krause, K. Moelling, R. Volkmer-Engert, H. Oschkinat posted to domains pdz post-defense predictions spot-array by kgutwin on 2009-05-20 05:37:05 as
	PDZ domain proteins: Scaffolds for signaling complexes [My Copy] Current Biology, Vol. 7, No. 12. (01 December 1997), pp. R770-R773. by Rama Ranganathan, Elliott M. Ross posted to domains pdz post-defense by kgutwin on 2009-05-20 05:32:04 as
	Gene families: the taxonomy of protein paralogs and chimeras. [My Copy] Science, Vol. 278, No. 5338. (24 October 1997), pp. 609-614. by S. Henikoff, E. A. Greene, S. Pietrokovski, P. Bork, T. K. Attwood, L. Hood posted to domains post-defense by kgutwin on 2009-05-20 05:19:32 as along with 4 people and 1 group bpcusack Einat ruvido svdate structural_bioinformatics
	Physical basis of a protein-DNA recognition code [My Copy] Current Opinion in Structural Biology, Vol. 7, No. 1. (February 1997), pp. 117-125. by Y. Choo posted to domains post-defense zincfinger by kgutwin on 2009-05-20 05:16:44 as
	The limits of protein secondary structure prediction accuracy from multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 234, No. 4. (20 December 1993), pp. 951-957. by R. B. Russell, G. J. Barton posted to post-defense predictions secondary-structure by kgutwin on 2009-05-20 02:32:34 as
	Effective energy functions for protein structure prediction [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 139-145. by T. Lazaridis posted to design post-defense predictions statpot by kgutwin on 2009-05-19 19:19:12 as along with 1 person flbarroso
	Empirical potentials and functions for protein folding and binding. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 222-228. by S. Vajda, M. Sippl, J. Novotny posted to post-defense review statpot by kgutwin on 2009-05-19 19:17:05 as along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
	A new approach to protein fold recognition [My Copy] Nature, Vol. 358, No. 6381. (2 July 1992), pp. 86-89. by D. T. Jones, W. R. Taylort, J. M. Thornton posted to statpot threading post-defense by kgutwin on 2009-05-19 19:06:44 as along with 4 people georgwachter chad_davis winterschlaefer janasont
	Interrogating protein interaction networks through structural biology. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901. by P. Aloy, R. B. Russell posted to interactions interprets predictions statpot post-defense by kgutwin on 2009-05-19 19:02:58 as along with 13 people and 3 groups tomhebbron bpcusack ana barry baaden bicko lfriedl chad_davis henschel ruvido cjeans tale Evangelia structural_bioinformatics kdl Bioinformatics
	InterPreTS: protein interaction prediction through tertiary structure. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 161-162. by P. Aloy, R. B. Russell posted to interactions interprets predictions statpot structure post-defense by kgutwin on 2009-05-19 18:52:27 as along with 6 people baaden bicko chad_davis henschel ruvido Pao-Yang
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to design post-defense predictions rosetta structure by kgutwin on 2009-05-19 04:23:35 as along with 10 people bmduggan Diego_Prada onufriev apaydin dfgreen jwm hmk heymiki kevinchannon ca3295
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to ab-initio post-defense predictions rosetta structure by kgutwin on 2009-05-19 04:17:00 as along with 11 people and 4 groups ucbcjbm paddydu BragilMassoud ana barry thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Tertiary templates for proteins 1Use of packing criteria in the enumeration of allowed sequences for different structural classes [My Copy] Journal of Molecular Biology*, Vol. 193, No. 4. (20 February 1987), pp. 775-791. by J. Ponder, F. Richards posted to historical need-pdf post-defense prediction structure threading by kgutwin on 2009-05-19 03:54:08 as along with 1 person carlosjavierna
	A method to identify protein sequences that fold into a known three-dimensional structure. [My Copy] Science, Vol. 253, No. 5016. (12 July 1991), pp. 164-170. by J. U. Bowie, R. Lüthy, D. Eisenberg posted to design prediction profiles structure post-defense by kgutwin on 2009-05-19 03:27:20 as along with 3 people fisherp apaydin chad_davis
	Principles of helix-helix packing in proteins: the helical lattice superposition model. [My Copy] J Mol Biol, Vol. 255, No. 3. (26 January 1996), pp. 536-553. by D. Walther, F. Eisenhaber, P. Argos posted to helix-packing post-defense by kgutwin on 2009-05-19 03:05:21 as along with 1 person chgjb
	Structure of proteins: packing of alpha-helices and pleated sheets. [My Copy] Proc Natl Acad Sci U S A, Vol. 74, No. 10. (October 1977), pp. 4130-4134. by C. Chothia, M. Levitt, D. Richardson posted to helix-packing historical post-defense by kgutwin on 2009-05-19 02:58:47 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding [My Copy] Journal of Molecular Biology, Vol. 289, No. 2. (04 June 1999), pp. 205-209. by J. Myers posted to coiled-coils folding post-defense by kgutwin on 2009-05-18 21:14:39 as
	Packing of alpha-helices: geometrical constraints and contact areas. [My Copy] Journal of molecular biology, Vol. 119, No. 4. (15 March 1978), pp. 537-555. by T. J. Richmond, F. M. Richards posted to helix-packing historical post-defense by kgutwin on 2009-05-18 16:10:33 as
	The Zipper-Like Folding of Collagen Triple Helices and the Effects of Mutations that Disrupt the Zipper [My Copy] Annual Review of Biophysics and Biophysical Chemistry, Vol. 20, No. 1. (1991), pp. 137-152. by J. Engel, D. J. Prockop posted to collagen folding post-defense by kgutwin on 2009-05-17 03:42:22 as

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predictions	28
domains	12
secondary-structure	10
structure	10
helix-packing	8
review	8
kinase	6
need-pdf	6
rosetta	6
specificity	6
ab-initio	5
folding	5
snare	5
statpot	5
chou-fasman	4
collagen	4
coiled-coils	3
design	3
historical	3
interactions	3
pdz	3
scaffold	3
sh3	3
zincfinger	3
casp	2
gor	2
interprets	2
npc	2
potential	2
prediction	2
sh2	2
tasser	2
threading	2
tropomyosin	2
alignment	1
amber	1
antiparallel	1
bzip	1
calmodulin	1
charmm	1
database	1
docking	1
ef-hand	1
homology-model	1
ism	1
kinetics	1
profiles	1
psipred	1
spot-array	1
yeast-2-hybrid	1

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