wouterboomsma's protein-structure [68 articles] Export Sort

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	P-SEA: a new efficient assignment of secondary structure from Calpha trace of proteins [My Copy] Comput. Appl. Biosci., Vol. 13, No. 3. (1 June 1997), pp. 291-295. by G. Labesse, N. Colloc'h, J. Pothier, J. P. Mornon posted to protein-structure secondary-structure by wouterboomsma on 2007-10-03 15:16:01 as along with 3 people dfdong thamelry j3xucite
	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 protein-structure secondary-structure by wouterboomsma on 2007-09-05 13:09:57 as along with 33 people dfdong barmak7282 Vadikus j3xucite scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna mijam wqia007 dsmueller niallhaslam saunders jwm sebk Diego_Prada pjcite kaarsinogen lna chad_davis penka ffranca dgront choonpeng rabio gisle medic0747 martainn chgjb mschofie marti
	Protein secondary structure prediction based on position-specific scoring matrices. [My Copy] Journal of molecular biology, Vol. 292, No. 2. (17 September 1999), pp. 195-202. by D. T. Jones posted to protein-structure secondary-structure by wouterboomsma on 2007-09-05 12:57:13 as along with 11 people rpetrenko kgutwin pjcite chad_davis j3xucite dgront rabio rph dandaman saunders granujilla
	Stereochemistry of polypeptide chain configurations. [My Copy] Journal of molecular biology, Vol. 7 (July 1963), pp. 95-99. by G. N. RAMACHANDRAN, C. RAMAKRISHNAN, V. SASISEKHARAN posted to protein-structure by wouterboomsma on 2007-09-05 12:26:46 as along with 7 people stharward kumar_physics yangjustinc reyez cen4ik jwm Diego_Prada
	Dissecting contact potentials for proteins: Relative contributions of individual amino acids. [My Copy] Proteins (19 July 2007) by N-V V. Buchete, J E E. Straub, D Thirumalai posted to energy-function protein-structure by wouterboomsma on 2007-07-30 09:22:06 as along with 2 people RamuAnandakrishnan kgutwin
	Characterization of protein-folding pathways by reduced-space modeling. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 30. (24 July 2007), pp. 12330-12335. by Sebastian Kmiecik, Andrzej Kolinski posted to folding-pathways protein-structure by wouterboomsma on 2007-07-30 09:20:45 as along with 6 people saunders carlosjavierna mijam mkurc sekmi nh
	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 protein-structure by wouterboomsma on 2007-07-30 09:15:33 as along with 4 people onufriev aqeel cdeane ARobson
	Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field [My Copy] BMC Structural Biology, Vol. 7, No. 1. (29 June 2007), 43. by Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski posted to protein-structure by wouterboomsma on 2007-07-09 10:56:24 as along with 3 people mijam rabio sekmi
	A coarse-grained protein force field for folding and structure prediction [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. 2. (28 June 2007), pp. 394-408. by Julien Maupetit, P. Tuffery, Philippe Derreumaux posted to energy-function protein-structure by wouterboomsma on 2007-07-09 10:54:21 as along with 2 people edws choonpeng
	Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo. [My Copy] J Chem Phys, Vol. 126, No. 22. (14 June 2007) by J. Zhang, S. C. Kou, J. S. Liu posted to mcmc protein-structure by wouterboomsma on 2007-07-09 10:51:36 as along with 1 person huyun110
	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 protein-structure review by wouterboomsma on 2007-07-09 10:49:08 as along with 8 people flbarroso onufriev cat_worth cactus Jporci cdeane kalicuta sebk
	ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. [My Copy] Nucleic Acids Res (21 May 2007) by Markus Wiederstein, Manfred J J. Sippl posted to error-detection protein-structure by wouterboomsma on 2007-07-09 10:37:44 as
	Ab initio protein structure prediction using chunk-TASSER. [My Copy] Biophys J (11 May 2007) by Hongyi Zhou, Jeffrey Skolnick posted to protein-structure by wouterboomsma on 2007-07-09 10:33:23 as along with 1 person huyun110
	"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. [My Copy] J Biosci, Vol. 32, No. 1. (January 2007), pp. 51-70. by A. G. De Brevern, C. Etchebest, C. Benros, S. Hazout posted to local-structure protein-structure by wouterboomsma on 2007-05-15 11:03:00 as along with 1 person j3xucite
	Protein structure prediction aided by geometrical and probabilistic constraints. [My Copy] Journal of computational chemistry, Vol. 28, No. 12. (20 September 2007), pp. 1943-1952. by Gaurav Porwal, Swapnil Jain, S. Dhilly Babu, Deepak Singh, Hemant Nanavati, Santosh Noronha posted to protein-structure by wouterboomsma on 2007-05-15 11:02:40 as along with 1 person rasfonseca
	Protein structure prediction: Combining de novo modeling with sparse experimental data. [My Copy] J Comput Chem (6 March 2007) by Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski posted to experimental-data protein-structure by wouterboomsma on 2007-05-15 10:53:27 as along with 1 person dgront
	Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates [My Copy] Journal of Computational Chemistry, Vol. 28, No. 9. (15 July 2007), pp. 1593-1597. by Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski posted to protein-structure representation by wouterboomsma on 2007-05-15 10:52:30 as along with 7 people Gabriel439 mcbla rabio j3xucite dgront sekmi mijam
	HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins1 [My Copy] Journal of Molecular Biology, Vol. 301, No. 1. (04 August 2000), pp. 173-190. by Christopher Bystroff, Vesteinn Thorsson, David Baker posted to fragments protein-structure by wouterboomsma on 2007-02-27 14:03:55 as along with 5 people and 1 group jwm j3xucite dgront rabio wenhan MBLAB
	Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study [My Copy] PNAS, Vol. 103, No. 9. (28 February 2006), pp. 3141-3146. by George Chikenji, Yoshimi Fujitsuka, Shoji Takada posted to fragments protein-structure by wouterboomsma on 2007-02-26 18:13:08 as along with 5 people flbarroso xingwuliu eckart_bindewald rsantana saunders
	Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. [My Copy] Proteins, Vol. 18, No. 4. (April 1994), pp. 353-366. by A. Kolinski, J. Skolnick posted to lattice protein-structure by wouterboomsma on 2007-02-26 17:33:07 as along with 1 person flbarroso
	Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. [My Copy] Proteins, Vol. 18, No. 4. (April 1994), pp. 338-352. by A. Kolinski, J. Skolnick posted to lattice protein-structure by wouterboomsma on 2007-02-26 17:28:38 as along with 3 people flbarroso dgront iantunbridge
	An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. [My Copy] Proc Natl Acad Sci U S A, Vol. 91, No. 10. (10 May 1994), pp. 4436-4440. by J. U. Bowie, D. Eisenberg posted to fragments protein-structure by wouterboomsma on 2007-02-26 13:11:30 as
	Folding proteins with a simple energy function and extensive conformational searching. [My Copy] Protein Sci, Vol. 5, No. 2. (February 1996), pp. 254-261. by K. Yue, K. A. Dill posted to protein-structure by wouterboomsma on 2007-02-26 12:35:49 as
	Determination of the conformation of folding initiation sites in proteins by computer simulation. [My Copy] Proteins, Vol. 23, No. 2. (October 1995), pp. 129-141. by F. Avbelj, J. Moult posted to protein-structure by wouterboomsma on 2007-02-26 11:57:08 as
	Automated structure prediction of weakly homologous proteins on a genomic scale [My Copy] PNAS, Vol. 101, No. 20. (18 May 2004), pp. 7594-7599. by Yang Zhang, Jeffrey Skolnick posted to protein-structure by wouterboomsma on 2007-02-26 10:45:29 as along with 5 people newton1234 babakap nigham j3xucite mirzazadeh
	LINUS: a hierarchic procedure to predict the fold of a protein. [My Copy] Proteins, Vol. 22, No. 2. (June 1995), pp. 81-99. by R. Srinivasan, G. D. Rose posted to local-structure protein-structure by wouterboomsma on 2007-02-23 19:53:51 as along with 1 person saunders
	Blind predictions of local protein structure in CASP2 targets using the I-sites library. [My Copy] Proteins, Vol. Suppl 1 (1997), pp. 167-171. by C. Bystroff, D. Baker posted to fragments protein-structure by wouterboomsma on 2007-02-22 20:01:06 as
	Some fundamental aspects of building protein structures from fragment libraries. [My Copy] Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650. by J. B. Holmes, J. Tsai posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:57:29 as along with 2 people and 2 groups barry eckart_bindewald structural_bioinformatics Bioinformatics
	Prediction of local structure in proteins using a library of sequence-structure motifs. [My Copy] Journal of molecular biology, Vol. 281, No. 3. (21 August 1998), pp. 565-577. by C. Bystroff, D. Baker posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:21:16 as along with 2 people jwm dgront
	All-atom ab initio folding of a diverse set of proteins. [My Copy] Structure, Vol. 15, No. 1. (January 2007), pp. 53-63. by J. S. Yang, W. W. Chen, J. Skolnick, E. I. Shakhnovich posted to protein-structure energy-function by wouterboomsma on 2007-02-05 11:42:46 as
	Prediction of structures of multidomain proteins from structures of the individual domains. [My Copy] Protein Sci (22 December 2006) by Andrew M M. Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker posted to protein-structure multi-domain by wouterboomsma on 2007-02-05 11:36:19 as along with 5 people dgront choonpeng zwang IrinaMoreira rph
	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 energy-function protein-structure by wouterboomsma on 2006-11-09 16:12:15 as along with 6 people Anis mijam kgutwin j3xucite cdeane dimka
	Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight. [My Copy] J Mol Model (Online) (7 October 2006) by Rajani R. Joshi, Vivekanand V. Samant posted to domain-finding protein-structure by wouterboomsma on 2006-10-16 17:54:35 as
	Novel approach for alpha-helical topology prediction in globular proteins: Generation of interhelical restraints. [My Copy] Proteins (6 October 2006) by S R R. McAllister, B E E. Mickus, J L L. Klepeis, C A A. Floudas posted to local-structure protein-structure by wouterboomsma on 2006-10-16 17:53:25 as
	Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2006), NA. by Philip Bradley, David Baker posted to protein-structure sampling by wouterboomsma on 2006-10-16 17:03:45 as along with 2 people zwang dgront
	Prediction of peptide structure: How far are we? [My Copy] Proteins (3 October 2006) by Annick Thomas, Sébastien Deshayes, Marc Decaffmeyer, Marie Hélène H. Van Eyck, Benoit Charloteaux, Robert Brasseur posted to protein-structure review by wouterboomsma on 2006-10-09 07:33:28 as
	Sampling Realistic Protein Conformations Using Local Structural Bias. [My Copy] PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006) by Thomas Hamelryck, John T T. Kent, Anders Krogh posted to protein-structure sampling by wouterboomsma on 2006-10-02 12:43:02 as along with 3 people xingwuliu j3xucite hmk
	Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (25 August 2006), pp. 362-372. by Bin-Guang Ma, Jian-Xiu Guo, Hong-Yu Zhang posted to folding-rate protein-structure by wouterboomsma on 2006-08-30 19:05:14 as along with 1 person melo_mcr
	A study of fragment-based protein structure prediction: biased fragment replacement for searching low-energy conformation. [My Copy] Genome Inform, Vol. 16, No. 2. (2005), pp. 104-113. by S. J. Park posted to fragments protein-structure by wouterboomsma on 2006-08-17 10:13:49 as
	Atom-by-atom analysis of global downhill protein folding [My Copy] Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321. by Mourad Sadqi, David Fushman, Victor Muã±oz posted to protein-structure by wouterboomsma on 2006-07-31 17:25:53 as along with 4 people and 2 groups marcius choonpeng gisle huyun110 BioinfoCIPF SGU-CIPF
	Atom-wise statistics and prediction of solvent accessibility in proteins. [My Copy] Biophys Chem (20 July 2006) by Y Hemajit H. Singh, M Michael M. Gromiha, Akinori Sarai, Shandar Ahmad posted to protein-structure solvent-exposure by wouterboomsma on 2006-07-26 11:41:52 as
	A contact energy function considering residue hydrophobic environment and its application in protein fold recognition. [My Copy] Genomics Proteomics Bioinformatics, Vol. 3, No. 4. (November 2005), pp. 218-224. by M. J. Duan, Y. H. Zhou posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:46:30 as
	Into the fold. Advances in technology and algorithms facilitate great strides in protein structure prediction. [My Copy] EMBO Rep, Vol. 7, No. 3. (March 2006), pp. 249-252. by P. Hunter posted to protein-structure review by wouterboomsma on 2006-07-24 14:43:07 as along with 1 person chad_davis
	HARMONY: a server for the assessment of protein structures. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by G. Pugalenthi, K. Shameer, N. Srinivasan, R. Sowdhamini posted to protein-structure quality-assessment servers by wouterboomsma on 2006-07-24 14:39:00 as along with 4 people viktor21614 bicko skhadar wilbur
	The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. [My Copy] Protein Eng Des Sel (14 July 2006) by Tianyun Liu, Ram Samudrala posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:37:00 as
	A model of local-minima distribution on conformational space and its application to protein structure prediction. [My Copy] Proteins (12 July 2006) by Hongzhi Li posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:29:37 as
	Progress in structure prediction of α-helical membrane proteins [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 4. (3 August 2006), pp. 496-504. by S. Fleishman, N. Bental posted to protein-structure review by wouterboomsma on 2006-07-24 14:26:30 as along with 2 people and 1 group viktor21614 xdeupi LabCompMed
	Ultra-Fast Evaluation of Protein Energies Directly from Sequence [My Copy] PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006), e63. by Gevorg Grigoryan, Fei Zhou, Steve R. Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating posted to energy-function protein-structure by wouterboomsma on 2006-07-24 13:56:42 as along with 3 people kevinchannon carlk chgjb
	Advances in homology protein structure modeling. [My Copy] Current protein & peptide science, Vol. 7, No. 3. (June 2006), pp. 217-227. by Z. Xiang posted to homology-modeling protein-structure by wouterboomsma on 2006-07-24 13:55:19 as along with 2 people mkotlyar flbarroso
	Potential for assessing quality of protein structure based on contact number prediction. [My Copy] Proteins (20 June 2006) by Takashi Ishida, Shugo Nakamura, Kentaro Shimizu posted to protein-structure quality-assessment by wouterboomsma on 2006-07-24 13:53:32 as

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