mcbla's library 54 articles Export

	A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics [My Copy] The Journal of Chemical Physics, Vol. 115, No. 3. (2001), pp. 1569-1574. by Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick posted to replica by mcbla on 2009-06-02 12:08:40 as along with 3 people dgront sikorski rabio
	Alignments grow, secondary structure prediction improves [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 2. (2002), pp. 197-205. by Dariusz Przybylski, Burkhard Rost posted to secondary_structure by mcbla on 2009-06-01 19:59:46 as along with 2 people rabio yoonk
	Review: protein secondary structure prediction continues to rise. [My Copy] J Struct Biol, Vol. 134, No. 2-3. (n 2001), pp. 204-218. by B. Rost posted to secondary_structure by mcbla on 2009-06-01 19:51:21 as along with 1 person dgront
	Equation of State Calculations by Fast Computing Machines [My Copy] The Journal of Chemical Physics, Vol. 21, No. 6. (1953), pp. 1087-1092. by Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth, Augusta H. Teller, Edward Teller posted to de_novo monte_carlo by mcbla on 2009-05-03 00:07:20 as along with 26 people eyliu zhaidong philipppixel iantunbridge wei flbarroso LGNR mrkn Diego_Prada jjray muraken scalptob ppeeling gale82 Jarosik apostola chad_davis tobin mkurc rabio gcalda Akimasa Bc91 guxiyou petermilner naegele
	3D-Jury: a simple approach to improve protein structure predictions. [My Copy] Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 1015-1018. by K. Ginalski, A. Elofsson, D. Fischer, L. Rychlewski posted to comparative_modeling by mcbla on 2009-04-30 22:52:56 as along with 6 people newton1234 rabio karbak dgront schuylrp mijam
	A model of evolutionary change in proteins [My Copy] Atlas of protein sequence and structure, Vol. 5, No. suppl 3. (1978), pp. 345-351. by M. O. Dayhoff, R. M. Schwartz, B. C. Orcutt posted to comparative_modeling by mcbla on 2009-04-29 20:51:30 as along with 1 person maria_hauser
	Amino acid substitution matrices from protein blocks. [My Copy] Proc Natl Acad Sci U S A, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to comparative_modeling by mcbla on 2009-04-29 20:25:26 as along with 1 person gisle
	Where did the BLOSUM62 alignment score matrix come from? [My Copy] Nature Biotechnology, Vol. 22, No. 8. (August 2004), pp. 1035-1036. by Sean R. Eddy posted to comparative_modeling by mcbla on 2009-04-29 20:13:54 as along with 7 people and 1 group svozil ziquje bicko gurkanbebek xiaobeizhao rabio reyez Bioinformatics
	Identification of common molecular subsequences [My Copy] Journal of Molecular Biology, Vol. 147, No. 1. (25 March 1981), pp. 195-197. by T. F. Smith, M. S. Waterman posted to comparative_modeling by mcbla on 2009-04-29 19:34:46 as along with 21 people rshe jengeldk maria_hauser jmanning2k cmor parnell adamnellis timflutre heliopais alessandroparini usagi-kirin creswick vavi bicko dgront rabio cjeans incovoma sujaikumar newton1234 bozdagd
	Modelowanie molekularne białek w oparciu o podobieństwo sekwencyjne i analogie strukturalne [My Copy] In Praca Doktorska (2002) by Piotr Rotkiewicz edited by Uniwersytet Warszawski posted to comparative_modeling tools by mcbla on 2009-04-27 14:30:22 as
	Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models [My Copy] Proteins: Structure, Function, and Genetics, Vol. 41, No. 1. (2000), pp. 86-97. by Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, Charles L. Brooks posted to tools by mcbla on 2009-04-27 13:56:13 as along with 1 person mijam
	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 84-90. by Andrzej Koliński, Janusz M. M. Bujnicki posted to cabs casp comparative_modeling strutcture_prediction by mcbla on 2009-04-27 13:16:18 as along with 4 people and 2 groups mijam nigham marcius dgront BioinfoCIPF SGU-CIPF
	Protein Folding: Flexible Lattice Models. [My Copy] Prog Theor Phys Suppl, Vol. 138 (2000), pp. 292-300. by A. Kolinski, P. Rotkiewicz, B. Ilkowski, J. Skolnick posted to no-tag by mcbla on 2009-04-27 09:55:13 as
	Defrosting the frozen approximation: PROSPECTOR - A new approach to threading [My Copy] Proteins: Structure, Function, and Genetics, Vol. 42, No. 3. (2001), pp. 319-331. by Jeffrey Skolnick, Daisuke Kihara posted to comparative_modeling threading by mcbla on 2009-04-26 00:32:48 as along with 1 person j3xucite
	Correlated mutations and residue contacts in proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 18, No. 4. (April 1994), pp. 309-317. by Ulrike Göbel, Chris Sander, Reinhard Schneider, Alfonso Valencia posted to contact by mcbla on 2009-04-26 00:28:59 as along with 9 people mgomes qluo RebeccaHamer gbart analogAI dgront cjeans jteyra Lombardo_7
	A general method applicable to the search for similarities in the amino acid sequence of two proteins. [My Copy] Journal of molecular biology, Vol. 48, No. 3. (March 1970), pp. 443-453. by S. B. Needleman, C. D. Wunsch posted to comparative_modeling by mcbla on 2009-04-25 23:44:07 as along with 16 people windman83 esyoun stsaft timflutre BioNica db344 DarkMars cawelsh9 sebk jwm dgront rabio incovoma yylin newton1234 Ema
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to comparative_modeling by mcbla on 2009-04-25 23:24:11 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to comparative_modeling by mcbla on 2009-04-25 23:20:50 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	Prediction of contact maps using support vector machines [My Copy] Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium on In Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium on (2003), pp. 26-33. by Ying Zhao, G. Karypis posted to contact svm by mcbla on 2009-04-25 22:52:46 as
	Contact prediction using mutual information and neural nets [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by George Shackelford, Kevin Karplus posted to contact review by mcbla on 2009-04-25 14:57:29 as along with 4 people RebeccaHamer cjeans RamuAnandakrishnan Lombardo_7
	A neural network based predictor of residue contacts in proteins [My Copy] Protein Eng., Vol. 12, No. 1. (1 January 1999), pp. 15-21. by P. Fariselli, R. Casadio posted to contact neural_network by mcbla on 2009-04-25 14:39:47 as along with 1 person cjeans
	Computational methods for the prediction of protein interactions [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 3. (1 June 2002), pp. 368-373. by A. Valencia posted to contact review by mcbla on 2009-04-25 13:57:34 as along with 4 people flbarroso IbnBio ruvido selrac
	Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives [My Copy] BMC Bioinformatics, Vol. 7 (16 November 2006), 503. by Petras J. Kundrotas, Emil G. Alexov posted to contact by mcbla on 2009-04-25 12:20:33 as along with 1 person Lombardo_7
	Predicting interresidue contacts using templates and pathways [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. S6. (2003), pp. 497-502. by Yu Shao, Christopher Bystroff posted to contact by mcbla on 2009-04-21 18:27:47 as along with 2 people babakap vavi
	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 cabs contact prediction by mcbla on 2009-04-21 17:48:01 as along with 3 people RamuAnandakrishnan sterl0601 j3xucite
	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 rosetta by mcbla on 2009-04-20 21:43:40 as along with 3 people kgutwin jwm Ema
	Assessment of CASP7 structure predictions for template free targets [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 57-67. by Ralf Jauch, Hock C. Yeo, Prasanna R. Kolatkar, Neil D. Clarke posted to casp by mcbla on 2009-04-20 21:31:41 as
	Critical assessment of methods of protein structure prediction-Round VII. [My Copy] Proteins, Vol. 69 Suppl 8, No. S8. (5 October 2007), pp. 3-9. by John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Burkhard Rost, Tim Hubbard, Anna Tramontano posted to casp by mcbla on 2009-04-20 21:06:37 as along with 5 people timhubbard mijam j3xucite nigham saunders
	A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 15, No. 3. (3 June 2005), pp. 285-289. by John Moult posted to casp by mcbla on 2009-04-20 20:33:41 as along with 12 people and 2 groups timhubbard flbarroso ujh nigham thaliana warlock6x3 marcius ffranca j3xucite dgront granujilla mingzhi BioinfoCIPF SGU-CIPF
	De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta [My Copy] Journal of the American Chemical Society, Vol. 124, No. 11. (1 March 2002), pp. 2723-2729. by Carol A. Rohl, David Baker posted to experimental_restraints nmr rosetta by mcbla on 2009-04-20 17:14:52 as along with 1 person dgront
	Przewidywanie struktury białek: Boltzmann i Darwin [My Copy] Kosmos, Vol. 54, No. 267-268. (2005) by Janusz M. Bujnicki posted to modeling review by mcbla on 2009-03-30 17:50:59 as
	Odgadywanie struktur życia [My Copy] Świat Nauki (February 2006), pp. 39-47. by Janusz M. Bujnicki, Krzysztof Ginalski, Andrzej Kolinski, Jan Kosinski posted to modeling review by mcbla on 2009-03-30 17:41:55 as
	How to Fold Graciously [My Copy] University of Illinois Press (1969), pp. 22-24. by C. Levinthal edited by J. T. P. Debrunner, E. Munck posted to protein_folding by mcbla on 2009-03-30 16:11:57 as
	The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 47 (15 September 1961), pp. 1309-1314. by C. B. Anfinsen, E. Haber, M. Sela, F. H. White posted to protein_folding by mcbla on 2009-03-30 15:58:18 as along with 3 people scampos cactus GeeSharpMinor
	Principles that govern the folding of protein chains. [My Copy] Science, Vol. 181, No. 96. (20 July 1973), pp. 223-230. by C. B. Anfinsen posted to protein_folding by mcbla on 2009-03-28 11:58:49 as along with 2 people warlock6x3 allmensch
	Practical lessons from protein structure prediction. [My Copy] Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891. by K. Ginalski, N. V. Grishin, A. Godzik, L. Rychlewski posted to comparative_modeling by mcbla on 2009-03-25 13:44:40 as along with 8 people and 4 groups ana aalibes thaliana okarsligil marcius duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	A graph-theory algorithm for rapid protein side-chain prediction. [My Copy] Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2001-2014. by A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack posted to tools by mcbla on 2008-12-09 22:57:59 as along with 11 people oceanwind karbak nigham bicko blackbart bluvsh1 rsantana mijam jwm carlk newton1234
	Testing similarity measures with continuous and discrete protein models [My Copy] Proteins: Structure, Function, and Genetics, Vol. 50, No. 1. (2003), pp. 144-157. by Stefan Wallin, Jochen Farwer, Ugo Bastolla posted to rms by mcbla on 2008-12-06 23:06:00 as along with 2 people scampos jlh64
	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 D. Gront, S. Kmiecik, A. Kolinski posted to backbone tools by mcbla on 2008-12-01 23:11:18 as along with 7 people Gabriel439 rabio wouterboomsma j3xucite dgront sekmi mijam
	Utility library for structural bioinformatics [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 584-585. by Dominik Gront, Andrzej Kolinski posted to tools by mcbla on 2008-12-01 23:07:11 as along with 5 people mijam chad_davis dgront rabio Minty
	Comparative modeling for protein structure prediction [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 2. (27 February 2006), pp. 172-177. by Krzysztof Ginalski posted to comparative_modeling by mcbla on 2008-11-24 00:31:32 as along with 8 people mijam BragilMassoud kuhn rabio schuylrp ruvido insectopalo granujilla
	Evaluation of 3D-Jury on CASP7 models [My Copy] BMC Bioinformatics, Vol. 8 (21 August 2007), 304. by László Kaján, Leszek Rychlewski posted to casp comparative_modeling by mcbla on 2008-11-24 00:26:42 as along with 1 person rabio
	Knowledge-based potentials in protein design [My Copy] Current Opinion in Structural Biology In Membranes / Engineering and design, Vol. 16, No. 4. (August 2006), pp. 508-513. by Alan M. Poole, Rama Ranganathan posted to cabs comparative_modeling force_field interaction_hierarchy intro knowledge_based_potentials lattice_model lattice_models modeling mqap prediction protein protein_folding protein_structure review structure strutcture_prediction by mcbla on 2008-11-24 00:25:28 as along with 5 people and 2 groups flbarroso nigham marcius rabio bethbromley BioinfoCIPF SGU-CIPF
	Reduced models of proteins and their applications [My Copy] Polymer In Conformational Protein Conformations, Vol. 45, No. 2. (January 2004), pp. 511-524. by Andrzej Kolinski, Jeffrey Skolnick posted to cabs lattice_models by mcbla on 2008-11-24 00:21:41 as along with 2 people rabio iantunbridge
	Servers for protein structure prediction. [My Copy] Curr Opin Struct Biol (16 March 2006) by Daniel Fischer posted to mqap by mcbla on 2008-11-21 09:45:35 as along with 7 people kuhn chad_davis wouterboomsma dgront schuylrp granujilla Jporci
	Statistical potentials for fold assessment. [My Copy] Protein Sci, Vol. 11, No. 2. (February 2002), pp. 430-448. by F. Melo, R. Sanchez, A. Sali posted to mqap by mcbla on 2008-11-21 01:43:23 as along with 5 people and 2 groups krapnik mijam barry eckart_bindewald dgront structural_bioinformatics Bioinformatics
	Protein modeling and structure prediction with a reduced representation. [My Copy] Acta Biochim Pol, Vol. 51, No. 2. (2004), pp. 349-371. by A. Kolinski posted to cabs lattice_model lattice_models modeling prediction protein structure strutcture_prediction by mcbla on 2008-07-31 13:45:29 as along with 5 people vavi dgront rabio sekmi mijam
	Derivation of protein-specific pair potentials based on weak sequence fragment similarity. [My Copy] Proteins, Vol. 38, No. 1. (1 January 2000), pp. 3-16. by J. Skolnick, A. Kolinski, A. Ortiz posted to comparative_modeling force_field by mcbla on 2007-07-08 11:20:54 as along with 2 people and 2 groups marcius dgront BioinfoCIPF SGU-CIPF
	Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. [My Copy] J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501. by M. J. Sippl posted to force_field by mcbla on 2007-07-08 11:17:32 as along with 3 people and 2 groups marcius dgront aengisch BioinfoCIPF SGU-CIPF
	In quest of an empirical potential for protein structure prediction. [My Copy] Curr Opin Struct Biol., Vol. 16, No. 2. (April 2006), pp. 166-171. by J. Skolnick posted to force_field review by mcbla on 2007-07-08 10:49:54 as along with 1 person dgront

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comparative_modeling	16
contact	8
force_field	8
review	7
casp	6
cabs	5
protein_folding	5
tools	5
modeling	4
lattice_models	3
mqap	3
prediction	3
strutcture_prediction	3
interaction_hierarchy	2
intro	2
knowledge_based_potentials	2
lattice_model	2
protein	2
protein_structure	2
rosetta	2
secondary_structure	2
structure	2
backbone	1
de_novo	1
experimental_restraints	1
monte_carlo	1
neural_network	1
nmr	1
replica	1
rms	1
svm	1
threading	1

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