cdeane's library 79 articles Export

	Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. [My Copy] BMC Bioinformatics, Vol. 6 (28 June 2005) by W. Boomsma, T. Hamelryck posted to cyclic descent loop modelling by cdeane on 2008-10-22 18:33:38 as along with 3 people pansapiens vavi wouterboomsma
	Choosing BLAST options for better detection of orthologs as reciprocal best hits [My Copy] Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 319-324. by Gabriel Moreno-Hagelsieb, Kristen Latimer posted to alignment homologs by cdeane on 2008-09-19 12:13:44 as along with 10 people operon treangen druvus natstreet guhjy cjeans winterschlaefer renatomilani mclarenv cerca
	All are not equal: A benchmark of different homology modeling programs [My Copy] Protein Sci, Vol. 14, No. 5. (1 May 2005), pp. 1315-1327. by Bjorn Wallner, Arne Elofsson posted to modelling by cdeane on 2008-09-02 08:01:17 as along with 6 people and 2 groups karbak marcius eweaver BioNica rsantana hmk BioinfoCIPF SGU-CIPF
	An evaluation of automated homology modelling methods at low target template sequence similarity [My Copy] Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1901-1908. by James A. Dalton, Richard M. Jackson posted to modelling by cdeane on 2008-09-02 08:00:50 as along with 5 people chad_davis biehl neils pansapiens marti
	Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network [My Copy] PLoS Biol, Vol. 4, No. 10. (19 September 2006), e317. by Nizar N. Batada, Teresa Reguly, Ashton Breitkreutz, et al.Lorrie Boucher, Bobby-Joe Breitkreutz, Laurence D. Hurst, Mike Tyers posted to hub networks party by cdeane on 2008-07-16 11:41:00 as along with 8 people mgomes lawraga aswin jpoyatos iris_2001 winterschlaefer Evangelia carlk
	Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction [My Copy] PLoS Biology, Vol. 5, No. 6. (1 June 2007), e154. by Nizar N. Batada, Teresa Reguly, Ashton Breitkreutz, et al.Lorrie Boucher, Bobby-Joe Breitkreutz, Laurence D. Hurst, Mike Tyers posted to hub networks party by cdeane on 2008-07-16 11:39:55 as along with 4 people lawraga winterschlaefer carlk antonkratz
	Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers [My Copy] Evolutionary Bioinformatics, Vol. 4 (2008), pp. 203-216. by Najl posted to no-tag by cdeane on 2008-07-16 11:35:57 as
	OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing [My Copy] Journal of Molecular Biology, Vol. 376, No. 1. (8 February 2008), pp. 288-301. by Mingyang Lu, Athanasios D. Dousis, Jianpeng Ma posted to folding modelling potential by cdeane on 2008-07-11 10:17:42 as along with 3 people mijam j3xucite kgutwin
	A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis [My Copy] PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98. by Julian R. Hughes, Ana M. Meireles, Katherine H. Fisher, et al.Angel Garcia, Philip R. Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G. Wakefield posted to interactions microtubule networks by cdeane on 2008-04-23 14:19:22 as along with 1 person and 1 group barry Bioinformatics
	Integrating physical and genetic maps: from genomes to interaction networks [My Copy] Nature Reviews Genetics, Vol. 8, No. 9. (01 September 2007), pp. 699-710. by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker posted to interactions motifs networks by cdeane on 2008-04-23 14:15:05 as along with 20 people and 4 groups Jporci dakelley chasmand mtaschuk Zephyrus druvus yyby misonneh giovenko bpcusack guhjy balicea dchughes sebastien_vigneau grahamc joepickrell zwang shikin lh1 carlk Roswell Cancer Crosstalk Bioinformatics G4ID Genetics-of-Gambling
	Modeling cellular machinery through biological network comparison. [My Copy] Nature biotechnology, Vol. 24, No. 4. (06 April 2006), pp. 427-433. by Roded Sharan, Trey Ideker posted to interactions motifs networks by cdeane on 2008-04-23 14:10:54 as along with 22 people and 1 group chica akshayk sergiun cswinburne kaarsinogen isimpson tmmurali kuhn tuck yas balajis wnpx ma_ko gurkanbebek koller gcalda grahamc massivemayhem karfunkel mingzhi vietanh0 carlk T_lab
	A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues. [My Copy] Proteins (6 August 2007) by Hsiao-Mei M. Lu, Jie Liang posted to cotranslation folding lattice by cdeane on 2008-04-22 11:38:54 as along with 1 person and 1 group saunders OPIG
	Lattice simulations of cotranslational folding of single domain proteins. [My Copy] Proteins (5 September 2007) by Peiyu Wang, Dmitri K K. Klimov posted to cotranslation folding lattice by cdeane on 2008-04-22 11:38:16 as along with 1 person saunders
	Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. [My Copy] Journal of molecular biology, Vol. 377, No. 4. (4 April 2008), pp. 1265-1278. by Hua Cheng, Bong-Hyun H. Kim, Nick V. Grishin posted to fold folding by cdeane on 2008-04-22 11:34:53 as along with 2 people and 1 group martainn barry structural_bioinformatics
	Estimating the significance of sequence order in protein secondary structure and prediction. [My Copy] Bioinformatics, Vol. 16, No. 11. (November 2000), pp. 978-987. by J. Park, S. Dietmann, A. Heger, L. Holm posted to cotranslation modelling secondary structure by cdeane on 2008-04-01 14:57:29 as
	Selective Constraints, Amino Acid Composition, and the Rate of Protein Evolution [My Copy] Mol Biol Evol, Vol. 17, No. 4. (1 April 2000), pp. 656-664. by Nicolas J. Tourasse, Wen-Hsiung Li posted to folding membrane modelling by cdeane on 2008-03-13 11:37:37 as along with 3 people and 1 group penka RamuAnandakrishnan sebk Nie
	Remote homology detection of integral membrane proteins using conserved sequence features [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Andreas Bernsel, Håkan Viklund, Arne Elofsson posted to hmm membrane modelling structure by cdeane on 2008-03-13 11:33:56 as
	Accurate prediction of protein\|[ndash]\|protein interactions from sequence alignments using a Bayesian method [My Copy] Molecular Systems Biology, Vol. 4 (12 February 2008) by Lukas Burger, Erik van Nimwegen posted to interactions by cdeane on 2008-02-20 06:22:24 as along with 14 people iaolier robfsouza raik sjcockell kengg grahamc laughcry zwang biomcgary cabbagezs roys gjuggler phoenixzxl pansapiens
	Loopholes and missing links in protein modeling. [My Copy] Protein Sci, Vol. 16, No. 9. (September 2007), pp. 1999-2012. by K. A. Rossi, C. A. Weigelt, A. Nayeem, S. R. Krystek posted to loop modelling by cdeane on 2008-02-20 06:19:59 as along with 2 people mijam LamBras
	Conformations of co-translational folding intermediates. [My Copy] Protein Pept Lett, Vol. 12, No. 2. (February 2005), pp. 189-195. by M. S. Evans, T. F. Clarke, P. L. Clark posted to cotranslation folding invivo by cdeane on 2008-02-06 00:39:45 as
	Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors. [My Copy] Proteins (13 February 2006) by Jinfeng Zhang, Rong Chen, Jie Liang posted to cotranslation folding potential simplemodel by cdeane on 2008-02-06 00:23:05 as along with 3 people flbarroso RamuAnandakrishnan wouterboomsma
	An assessment of the uses of homologous interactions [My Copy] Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 689-695. by Ramazan Saeed, Charlotte Deane posted to interactions by cdeane on 2008-01-18 18:01:16 as along with 11 people snow_dragon carlk lawraga winterschlaefer chad_davis grahamc cjeans laughcry mingzhi Pao-Yang samesense
	From the Cover: Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors [My Copy] PNAS, Vol. 104, No. 8. (20 February 2007), pp. 2885-2890. by Roger P. Alexander, Igor B. Zhulin posted to chemotaxis interactions by cdeane on 2008-01-15 14:23:05 as along with 2 people chrn RebeccaHamer
	Bio3d: an R package for the comparative analysis of protein structures. [My Copy] Bioinformatics (29 August 2006) by Barry J J. Grant, Ana P C P. Rodrigues, Karim M M. Elsawy, J Andrew A. McCammon, Leo S D S. Caves posted to comparison r structure by cdeane on 2008-01-09 15:56:21 as along with 9 people and 2 groups dfdong dswan gisle ana barry Einat plofje krishnaJCSG insectopalo structural_bioinformatics Bioinformatics
	Evidence for dynamically organized modularity in the yeast protein-protein interaction network. [My Copy] Nature, Vol. 430, No. 6995. (1 July 2004), pp. 88-93. by Jing-Dong D. Han, Nicolas Bertin, Tong Hao, et al.Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. Walhout, Michael E. Cusick, Frederick P. Roth, Marc Vidal posted to date interactions party by cdeane on 2008-01-09 14:15:44 as along with 29 people and 2 groups colmryan mgomes saket lawraga diamantis davidecellai dragonrez lfriedl balajis yoh j3xucite kintoki koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes winterschlaefer Evangelia shung phoenixzxl stefanoallesina ellakat frohike shikin ksiek carlk kdl GeneGo
	Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. [My Copy] PLoS ONE, Vol. 2, No. 11. (2007) by G. Jin, S. Zhang, X. S. Zhang, L. Chen posted to date interactions party by cdeane on 2008-01-09 14:15:15 as along with 2 people lpfernandes cabbagezs
	Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights [My Copy] Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941. by Philip M. Kim, Long J. Lu, Yu Xia, Mark B. Gerstein posted to interactions sin structure by cdeane on 2008-01-09 14:14:34 as along with 23 people and 2 groups ucbcjbm pablocarb mgomes rsaito MatthiasReimann cerca bicko lfriedl chad_davis Einat tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes Pao-Yang phoenixzxl carlk paolomarcatili saket structural_bioinformatics kdl
	Protein stability promotes evolvability [My Copy] PNAS, Vol. 103, No. 15. (11 April 2006), pp. 5869-5874. by Jesse D. Bloom, Sy T. Labthavikul, Christopher R. Otey, Frances H. Arnold posted to folding stability by cdeane on 2007-11-22 12:35:59 as along with 10 people and 2 groups rklancer Retchless lna Einat penka cmm redelings BioNica Cristiano wilbur structural_bioinformatics FAB-lab
	Evolution favors protein mutational robustness in sufficiently large populations [My Copy] BMC Biology, Vol. 5, No. 1. (2007) by Jesse Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia Venturelli, Frances Arnold posted to folding stability by cdeane on 2007-11-22 12:34:33 as along with 3 people Pao-Yang bpcusack cambray
	Rigorous performance evaluation in protein structure modelling and implications for computational biology. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 453-458. by J. Moult posted to casp modelling by cdeane on 2007-11-22 09:47:29 as along with 2 people chad_davis wouterboomsma
	A topologically related singularity suggests a maximum preferred size for protein domains [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 621-629. by Joseph P. Zbilut, Gek H. Chua, Arun Krishnan, et al.Cecilia Bossa, Kristian Rother, Charles L. Webber, Alessandro Giuliani posted to folding modelling by cdeane on 2007-11-22 09:45:41 as along with 2 people choonpeng Pao-Yang
	The protein folding problem: when will it be solved? [My Copy] Curr Opin Struct Biol (13 June 2007) by Ken A A. Dill, S Banu B. Ozkan, Thomas R R. Weikl, John D D. Chodera, Vincent A A. Voelz posted to folding by cdeane on 2007-11-22 09:40:23 as along with 8 people flbarroso onufriev wouterboomsma cat_worth cactus Jporci kalicuta sebk
	Assessing model accuracy using the homology modeling automatically software. [My Copy] Proteins (19 July 2007) by Aneerban Bhattacharya, Zeba Wunderlich, Daniel Monleon, Roberto Tejero, Gaetano T T. Montelione posted to model modelling potential by cdeane on 2007-11-22 09:34:30 as along with 1 person cat_hutchinson68
	Protein folding by zipping and assembly. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992. by S. B. Ozkan, G. A. Wu, J. D. Chodera, K. A. Dill posted to folding md time by cdeane on 2007-11-21 15:54:16 as along with 4 people onufriev aqeel wouterboomsma ARobson
	Folding time predictions from all-atom replica exchange simulations. [My Copy] J Mol Biol, Vol. 372, No. 3. (21 September 2007), pp. 756-763. by S. Yang, J. N. Onuchic, A. E. García, H. Levine posted to folding time by cdeane on 2007-11-21 15:53:23 as
	QMEAN: A comprehensive scoring function for model quality assessment. [My Copy] Proteins (11 October 2007) by Pascal Benkert, Silvio C E C. Tosatto, Dietmar Schomburg posted to model potential by cdeane on 2007-11-21 15:52:28 as along with 4 people cat_hutchinson68 larian j3xucite sebk
	An efficient conformational sampling method for homology modeling. [My Copy] Proteins (11 October 2007) by Rongsheng Han, Alejandra Leo-Macias, Daniel Zerbino, Ugo Bastolla, Bruno Contreras-Moreira, Angel R R. Ortiz posted to md montecarlo teaching by cdeane on 2007-11-21 15:51:49 as along with 3 people dimka insectopalo sebk
	Protein stability imposes limits on organism complexity and speed of molecular evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 16152-16157. by Konstantin B. Zeldovich, Peiqiu Chen, Eugene I. Shakhnovich posted to evolution stability by cdeane on 2007-11-21 15:27:38 as along with 5 people bpcusack operon penka cjeans cactus
	An introduction to ROC analysis [My Copy] Pattern Recogn. Lett. In ROC Analysis in Pattern Recognition, Vol. 27, No. 8. (June 2006), pp. 861-874. by Tom Fawcett posted to roc by cdeane on 2007-11-21 15:26:24 as along with 35 people and 6 groups singhsh TLVincent module qluo q_w_e_r_t_y makrehchi Borelli mthomure sbarthelme jjrodriguez cen4ik jmetzen MosesCheckley ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos haiyeong AbnerCYH isimpson guhjy nherveg Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
	Saturating representation of loop conformational fragments in structure databanks [My Copy] BMC Structural Biology, Vol. 6 (04 July 2006), 15. by Narcis Fernandez-Fuentes, Andras Fiser posted to loop model modelling by cdeane on 2007-11-21 15:19:45 as along with 3 people iakes vavi saunders
	ArchPRED: a template based loop structure prediction server. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by N. Fernandez-Fuentes, J. Zhai, A. Fiser posted to loop model modelling by cdeane on 2007-11-21 15:19:25 as along with 3 people mijam vavi eckart_bindewald
	Long loop prediction using the protein local optimization program. [My Copy] Proteins (22 August 2006) by Kai Zhu, David L L. Pincus, Suwen Zhao, Richard A A. Friesner posted to loop model modelling by cdeane on 2007-11-21 15:18:56 as along with 2 people mijam vavi
	Statistical potential for assessment and prediction of protein structures. [My Copy] Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2507-2524. by M. Y. Shen, A. Sali posted to model potential by cdeane on 2007-11-21 15:18:29 as along with 6 people Anis mijam kgutwin wouterboomsma j3xucite dimka
	Scoring function accuracy for membrane protein structure prediction. [My Copy] Proteins, Vol. 68, No. 1. (1 July 2007), pp. 67-75. by C. Gao, H. A. Stern posted to membrane model by cdeane on 2007-11-21 15:17:20 as along with 1 person sebk
	Prediction of protein loop geometries in solution. [My Copy] Proteins, Vol. 69, No. 1. (1 October 2007), pp. 69-74. by C. S. Rapp, T. Strauss, A. Nederveen, G. Fuentes posted to loop model by cdeane on 2007-11-21 15:16:44 as
	Loop modeling: sampling, filtering, and scoring. [My Copy] Proteins (29 August 2007) by Cinque S S. Soto, Marc Fasnacht, Jiang Zhu, Lucy Forrest, Barry Honig posted to loop model by cdeane on 2007-11-21 15:16:03 as along with 2 people and 1 group mijam granujilla OPIG
	Modeling protein loops with knowledge-based prediction of sequence-structure alignment. [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2836-2842. by H. P. Peng, A. S. Yang posted to loop model by cdeane on 2007-11-21 15:15:32 as along with 2 people mijam carlosjavierna
	Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. [My Copy] Proteins (17 September 2007) by Riccardo M M. Bennett-Lovsey, Alex D D. Herbert, Michael J E J. Sternberg, Lawrence A A. Kelley posted to loop modelling by cdeane on 2007-11-21 15:14:15 as along with 1 person j3xucite
	A molecular model for the origin of protein translation in an RNA world. [My Copy] J Theor Biol, Vol. 243, No. 3. (7 December 2006), pp. 393-406. by W. R. Taylor posted to fold rna by cdeane on 2007-11-21 15:12:53 as along with 1 group OPIG
	Topological accessibility shows a distinct asymmetry in the folds of betaalpha proteins. [My Copy] FEBS Lett, Vol. 580, No. 22. (2 October 2006), pp. 5263-5267. by W. R. Taylor posted to cotranslation fold by cdeane on 2007-11-21 15:12:20 as

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modelling	15
folding	13
model	12
interactions	9
loop	9
cotranslation	6
stability	6
fold	5
networks	5
potential	5
lattice	4
party	4
structure	4
membrane	3
date	2
evolution	2
hub	2
md	2
motifs	2
time	2
alignment	1
casp	1
chemotaxis	1
comparison	1
cyclic	1
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descent	1
hmm	1
homologs	1
invivo	1
knots	1
microtubule	1
montecarlo	1
r	1
rna	1
roc	1
secondary	1
simplemodel	1
sin	1
teaching	1

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