j3xucite's library 464 articles Export

	Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features [My Copy] Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637. by Wolfgang Kabsch, Christian Sander posted to no-tag by j3xucite on 2009-10-21 17:26:46 as along with 31 people Vadikus scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna mijam wqia007 dsmueller niallhaslam saunders jwm sebk Diego_Prada pjcite kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng rabio gisle medic0747 martainn chgjb mschofie marti
	A Probabilistic Graphical Model for Ab Initio Folding [My Copy] In RECOMB 2'09: Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (2009), pp. 59-73. by Feng Zhao, Jian Peng, Joe Debartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu posted to no-tag by j3xucite on 2009-10-21 04:04:58 as
	MUFOLD: A new solution for protein 3D structure prediction [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2009), NA. by Jingfen Zhang, Qingguo Wang, Bogdan Barz, et al.Zhiquan He, Ioan Kosztin, Yi Shang, Dong Xu posted to no-tag by j3xucite on 2009-10-17 17:25:08 as along with 1 person babakap
	I-TASSER: Fully automated protein structure prediction in CASP8. [My Copy] Proteins, Vol. 77, No. S9. (21 August 2009), pp. 100-113. by Yang Zhang posted to no-tag by j3xucite on 2009-10-17 17:10:15 as along with 2 people maria_hauser reyez
	Structure prediction for CASP8 with all-atom refinement using Rosetta [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (20 July 2009), NA. by Srivatsan Raman, Robert Vernon, James Thompson, et al.Michael Tyka, Ruslan Sadreyev, Jimin Pei, David Kim, Elizabeth Kellogg, Frank DiMaio, Oliver Lange, Lisa Kinch, Will Sheffler, Bong-Hyun Kim, Rhiju Das, Nick V. Grishin, David Baker posted to no-tag by j3xucite on 2009-10-17 17:02:21 as along with 1 person timhubbard
	Analysis of CASP8 targets, predictions and assessment methods [My Copy] Database, Vol. 2009, No. 0. (28 April 2009), bap003. by Shuoyong Shi, Jimin Pei, Ruslan I. Sadreyev, et al.Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin posted to casp8 by j3xucite on 2009-08-11 18:12:34 as
	Prediction of global and local quality of CASP8 models by MULTICOM series [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Jianlin Cheng, Zheng Wang, Allison N. Tegge, Jesse Eickholt posted to qualityassessment by j3xucite on 2009-07-13 04:22:13 as
	Prediction of global and local model quality in CASP8 using the ModFOLD server [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Liam J. Mcguffin posted to qualityassessment by j3xucite on 2009-07-13 04:15:02 as
	QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information [My Copy] BMC Structural Biology, Vol. 9, No. 1. (20 May 2009), 35. by Pascal Benkert, Torsten Schwede, Silvio Tosatto posted to assessment quality by j3xucite on 2009-07-13 04:10:07 as
	Improved protein structure selection using decoy-dependent discriminatory functions. [My Copy] BMC structural biology, Vol. 4 (18 June 2004) by K. Wang, B. Fain, M. Levitt, R. Samudrala posted to modelselection by j3xucite on 2009-06-01 03:53:36 as
	A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (24 March 2009), pp. 220-234. by Tianyun Liu, Jeremy A. Horst, Ram Samudrala posted to refinement by j3xucite on 2009-05-15 22:06:10 as along with 2 people and 1 group AliC newton1234 Orengo Group Journal Picks
	The Entropic Landscape of proteins revealing protein folding mechanism : Nature Precedings [My Copy] posted to entropyfolding by j3xucite on 2009-01-14 03:01:51 as along with 1 person vphan
	The meaning of alignment: lessons from structural diversity [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Walter Pirovano, Anton K. Feenstra, Jaap Heringa posted to structurealignment by j3xucite on 2009-01-05 22:12:23 as along with 13 people pimmy swtimmer dimka mhamada reyez treangen markusd nuin kshameer druvus chad_davis taguchi pansapiens
	Accelerating Resolution-of-the-Identity Second-Order Moller−Plesset Quantum Chemistry Calculations with Graphical Processing Units† [My Copy] The Journal of Physical Chemistry A, Vol. 112, No. 10. (1 March 2008), pp. 2049-2057. by Leslie Vogt, Roberto Olivares-Amaya, Sean Kermes, Yihan Shao, Carlos Amador-Bedolla, Alan Aspuru-Guzik posted to gpu by j3xucite on 2009-01-04 19:20:01 as along with 1 person ihaque
	A simple method to generate non-trivial alternate alignments of protein sequences. [My Copy] Journal of molecular biology, Vol. 219, No. 4. (20 June 1991), pp. 727-732. by M. A. Saqi, M. J. Sternberg posted to alternativealignment by j3xucite on 2008-12-18 18:03:43 as
	Amino acid substitution matrices from protein blocks [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to blosum by j3xucite on 2008-12-17 21:53:40 as along with 12 people BioNica maria_hauser cmura alefox sebk cen4ik kaarsinogen dgront gurkanbebek Iden-J_GluR cjeans ashwinma
	Recognition of errors in three-dimensional structures of proteins. [My Copy] Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362. by M. J. Sippl posted to energy function by j3xucite on 2008-12-17 21:47:28 as along with 2 people medic0747 hmk
	Evaluating the absolute quality of a single protein model using structural features and support vector machines. [My Copy] Proteins (25 September 2008) by Zheng Wang, Allison N N. Tegge, Jianlin Cheng posted to modelqualityassessment by j3xucite on 2008-12-17 00:54:37 as along with 1 person pjcite
	Predicting residue-residue contact maps by a two-layer, integrated neural-network method [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2008), NA. by Bin Xue, Eshel Faraggi, Yaoqi Zhou posted to contactmapprediction by j3xucite on 2008-12-17 00:40:26 as along with 1 person Lombardo_7
	How well can the accuracy of comparative protein structure models be predicted? [My Copy] Protein science : a publication of the Protein Society, Vol. 17, No. 11. (November 2008), pp. 1881-1893. by D. Eramian, N. Eswar, M. Y. Shen, A. Sali posted to modelqualityassessment by j3xucite on 2008-12-16 22:57:34 as
	SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. [My Copy] PLoS ONE, Vol. 3, No. 6. (2008) by W. Zhang, S. Liu, Y. Zhou posted to threading by j3xucite on 2008-12-16 18:10:51 as along with 2 people svozil pjcite
	Assessment of RAPTOR's linear programming approach in CAFASP3 [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. S6. (2003), pp. 579-584. by Jinbo Xu, Ming Li posted to protein threading by j3xucite on 2008-12-16 16:44:52 as
	SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs [My Copy] BMC Structural Biology, Vol. 8 (03 December 2008), 52. by Arlo Randall, Pierre Baldi posted to modelqualityassess by j3xucite on 2008-12-14 17:50:14 as
	Profile Comparer: a program for scoring and aligning profile hidden Markov models [My Copy] Bioinformatics, Vol. 24, No. 22. (15 November 2008), pp. 2630-2631. by Martin Madera posted to no-tag by j3xucite on 2008-11-09 16:14:42 as along with 3 people and 1 group tonamswish djkt nuin iSEEM
	Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 3. (2006), pp. 587-600. by Yen H. Tan, He Huang, Daisuke Kihara posted to no-tag by j3xucite on 2008-11-08 17:10:39 as along with 1 person pjcite
	Fast accurate evaluation of protein solvent exposure [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 3. (2004), pp. 565-576. by Naigong Zhang, Chen Zeng, Ned S. Wingreen posted to no-tag by j3xucite on 2008-11-04 22:35:31 as along with 1 person hryk
	Configurational-bias sampling technique for predicting side-chain conformations in proteins [My Copy] Protein Sci, Vol. 15, No. 9. (1 September 2006), pp. 2029-2039. by Tushar Jain, David S. Cerutti, Andrew J. Mccammon posted to no-tag by j3xucite on 2008-11-04 22:04:39 as
	OPUS-Rota: A fast and accurate method for side-chain modeling [My Copy] Protein Sci, Vol. 17, No. 9. (1 September 2008), pp. 1576-1585. by Mingyang Lu, Athanasios D. Dousis, Jianpeng Ma posted to no-tag by j3xucite on 2008-11-04 16:58:03 as
	The effectiveness of position- and composition-specific gap costs for protein similarity searches [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i15-23. by Aleksandar Stojmirovic, Michael E. Gertz, Stephen F. Altschul, Yi-Kuo Yu posted to no-tag by j3xucite on 2008-11-03 17:16:13 as
	Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. [My Copy] Proteins, Vol. 54, No. 1. (1 January 2004), pp. 71-87. by J. O. Wrabl, N. V. Grishin posted to no-tag by j3xucite on 2008-11-03 16:36:06 as along with 4 people and 2 groups ana barry analogAI granujilla structural_bioinformatics Bioinformatics
	Modular DAG-RNN architectures for assembling coarse protein structures. [My Copy] J Comput Biol, Vol. 13, No. 3. (April 2006), pp. 631-650. by G. Pollastri, A. Vullo, P. Frasconi, P. Baldi posted to no-tag by j3xucite on 2008-11-02 21:38:03 as along with 1 person wouterboomsma
	Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs [My Copy] Genome Biology, Vol. 9, No. 4. (08 April 2008), R68. by Alejandro Panjkovich, Francisco Melo, Marc M. Renom posted to no-tag by j3xucite on 2008-11-02 05:39:48 as along with 2 people and 1 group sebk kgutwin KeatingJClub
	Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function [My Copy] Nucl. Acids Res., Vol. 32, No. 9. (20 May 2004), pp. 2838-2843. by Nalin C. Goonesekere, Byungkook Lee posted to no-tag by j3xucite on 2008-11-02 02:59:03 as along with 2 people and 2 groups ana analogAI structural_bioinformatics Bioinformatics
	Variable gap penalty for protein sequence structure alignment [My Copy] Protein Engineering, Design and Selection, Vol. 19, No. 3. (March 2006), pp. 129-133. by M. S. Madhusudhan, Marc A. Marti-Renom, Roberto Sanchez, Andrej Sali posted to no-tag by j3xucite on 2008-11-02 02:36:16 as along with 1 person BioNica
	Information and discrimination in pairwise contact potentials [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Armando D. Solis, S. Rackovsky posted to no-tag by j3xucite on 2008-10-30 16:18:42 as along with 2 people and 1 group kgutwin RamuAnandakrishnan KeatingJClub
	Property-based sequence representations do not adequately encode local protein folding information [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 4. (2007), pp. 785-788. by A. D. Solis, S. Rackovsky posted to no-tag by j3xucite on 2008-10-30 16:14:53 as
	Optimally informative backbone structural propensities in proteins. [My Copy] Proteins, Vol. 48, No. 3. (15 August 2002), pp. 463-486. by A. D. Solis, S. Rackovsky posted to no-tag by j3xucite on 2008-10-29 22:51:32 as along with 1 person karbak
	Local propensities and statistical potentials of backbone dihedral angles in proteins. [My Copy] J Mol Biol, Vol. 342, No. 2. (10 September 2004), pp. 635-649. by M. R. Betancourt, J. Skolnick posted to no-tag by j3xucite on 2008-10-29 17:33:22 as along with 2 people and 1 group Einat dgront structural_bioinformatics
	Efficient Monte Carlo trial moves for polypeptide simulations. [My Copy] J Chem Phys, Vol. 123, No. 17. (1 November 2005) by M. R. Betancourt posted to no-tag by j3xucite on 2008-10-29 04:15:45 as along with 2 people jwm dgront
	Orientational potentials extracted from protein structures improve native fold recognition. [My Copy] Protein Sci, Vol. 13, No. 4. (April 2004), pp. 862-874. by N. V. Buchete, J. E. Straub, D. Thirumalai posted to no-tag by j3xucite on 2008-10-26 21:05:13 as along with 2 people thamelry kgutwin
	Contact prediction in protein modeling. Scoring, folding and refinement of coarse-grained models. [My Copy] BMC Structural Biology, Vol. 8 (11 August 2008), 36. by Dorota Latek, Andrzej Kolinski posted to no-tag by j3xucite on 2008-10-24 07:01:26 as along with 3 people RamuAnandakrishnan mcbla sterl0601
	Advances in Rosetta protein structure prediction on massively parallel systems [My Copy] IBM J. Res. Dev., Vol. 52, No. 1. (2008), pp. 7-17. by S. Raman, B. Qian, D. Baker, R. C. Walker posted to no-tag by j3xucite on 2008-10-23 18:27:41 as along with 1 person kgutwin
	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 no-tag by j3xucite on 2008-10-23 04:05:34 as along with 4 people cat_hutchinson68 larian sebk cdeane
	Towards accurate residue–residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization [My Copy] PROTEINS: Structure, Function and Bioinformatics (2008) by R. Rajgaria, S. R. Mcallister, C. A. Floudas posted to no-tag by j3xucite on 2008-10-16 16:17:46 as
	Fragment-HMM: A New Approach To Protein Structure Prediction [My Copy] Protein Science (22 August 2008), ps.036442.108. by Shuai C. Li, Dongbo Bu, Jinbo Xu, Ming Li posted to no-tag by j3xucite on 2008-10-05 20:26:17 as along with 2 people mkotlyar xingwuliu
	Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays. [My Copy] Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, Vol. 6 (2007), pp. 335-342. by K. Ellrott, J. T. Guo, V. Olman, Y. Xu posted to no-tag by j3xucite on 2008-10-05 04:18:55 as
	Introduction to Protein Structure [My Copy] (15 January 1999) by Carl-Ivar Branden, John Tooze posted to no-tag by j3xucite on 2008-10-02 22:55:56 as along with 3 people faccioli reyez aalibes
	SPICKER: a clustering approach to identify near-native protein folds. [My Copy] J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 865-871. by Y. Zhang, J. Skolnick posted to no-tag by j3xucite on 2008-10-02 20:39:48 as along with 4 people and 1 group klexa oteri iakes nigham Structural Biology Group TorVergata
	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 no-tag by j3xucite on 2008-09-24 18:21:46 as along with 6 people kgutwin jwm balajis dgront bilab BioNica
	Simulated Annealing and Boltzmann Machines: A Stochastic Approach to Combinatorial Optimization and Neural Computing [My Copy] (1991) by Emile Aarts, Jan Korst posted to no-tag by j3xucite on 2008-09-24 18:16:01 as

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bibtex-import	190
protein	83
structure	41
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structurealignment	1
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