rabio's library 333 articles Export

	Generalized ensemble methods for de novo structure prediction [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1415-1420. by Alena Shmygelska, Michael Levitt posted to structure_prediction rosetta energy_function de_novo conformation_serching by rabio on 2009-10-12 10:09:19 as along with 5 people kentsis apaydin nurban hmk amishp
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted to structure_prediction review by rabio on 2009-10-12 09:15:34 as along with 17 people and 3 groups ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted to review docking by rabio on 2009-10-12 09:07:45 as along with 25 people and 4 groups ucbcjbm flbarroso csrocha oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Structural Biology Group TorVergata Bioinformatics TSRI_MGL insilicodrug
	Hierarchical modeling of protein interactions [My Copy] Journal of Molecular Modeling, Vol. 13, No. 6. (1 July 2007), pp. 691-698. by Mateusz Kurcinski, Andrzej Kolinski posted to docking by rabio on 2009-10-12 09:02:08 as along with 3 people mijam mkurc naitsabes
	Solvent dramatically affects protein structure refinement [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20239-20244. by Gaurav Chopra, Christopher M. Summa, Michael Levitt posted to solvent_model refinement potencial force_field energy_minimization by rabio on 2009-09-29 14:05:09 as along with 7 people and 4 groups pavanghatty mijam dgront barry sobolevnrm biehl itmeson structural_bioinformatics McCammon Bioinformatics baker-group
	Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization [My Copy] Nucleic Acids Res, Vol. 33, No. 14. (2005), pp. 4496-4506. by Erik Lindahl, Marc Delarue posted to docking refinement by rabio on 2009-08-03 16:04:11 as along with 1 person baaden
	Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 2. (2005), pp. 263-268. by Graham R. Smith, Paul W. Fitzjohn, Christopher S. Page, Paul A. Bates posted to docking by rabio on 2009-08-03 16:02:28 as
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to tools by rabio on 2009-08-03 15:45:17 as along with 22 people and 2 groups softsimu parnell oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Open source clustering software. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 9. (12 June 2004), pp. 1453-1454. by M. J. de Hoon, S. Imoto, J. Nolan, S. Miyano posted to clustering tools by rabio on 2009-07-05 17:37:45 as along with 25 people and 7 groups dakelley klexa oteri arlam ilyashl matterhorn cswinburne mtagaya macowell davidbroadhurst eme oilcan rahul Ayest balajis piscinero metamerist digisoki wnpx rafamayo atopcu ccr calu karlmicha chad_davis Structural Biology Group TorVergata Fluid-Mechanics-and-Thermal-Science-Research astro SRL Computational_Systems_Biology XMLDataManagement BUiGEM
	Accurate modeling of protein conformation by automatic segment matching. [My Copy] J Mol Biol, Vol. 226, No. 2. (20 July 1992), pp. 507-533. by M. Levitt posted to structure_fragments structure_prediction by rabio on 2009-06-25 15:21:30 as along with 4 people mijam warlock6x3 dgront granujilla
	Modelling the polypeptide backbone with 'spare parts' from known protein structures [My Copy] Protein Eng., Vol. 2, No. 5. (1 January 1989), pp. 335-345. by Michel Claessens, Eric van Cutsem, Ignace Lasters, Shoshana Wodak posted to structure_fragments structure_prediction by rabio on 2009-06-25 15:20:21 as along with 2 people j3xucite dgront
	Stanislaw M. Ulam's contributions to theoretical theory [My Copy] Letters in Mathematical Physics, Vol. 10, No. 2. (1 June 1985), pp. 231-242. by William A. Beyer, Peter H. Sellers, Michael S. Waterman posted to history_of_science by rabio on 2009-06-17 16:51:55 as
	Some biological sequence metrics [My Copy] Advances in Mathematics, Vol. 20, No. 3. (June 1976), pp. 367-387. by M. Waterman, T. Smith, W. Beyer posted to sequence_alignment by rabio on 2009-06-17 16:26:55 as
	An improved algorithm for matching biological sequences [My Copy] J Mol Biol, Vol. 162, No. 3. (15 December 1982), pp. 705-708. by Osamu Gotoh posted to sequence_alignment by rabio on 2009-06-17 10:36:43 as along with 5 people mmartin sebk vavi adijr jofiel
	Optimal sequence alignment using affine gap costs [My Copy] Bulletin of Mathematical Biology, Vol. 48, No. 5. (1 September 1986), pp. 603-616. by Stephen Altschul, Bruce Erickson posted to sequence_alignment by rabio on 2009-06-17 10:10:19 as
	Nanometer properties of oceanic polymetallic nodules and cobalt-rich crusts [My Copy] Chinese Science Bulletin, Vol. 47, No. 15. (1 August 2002), pp. 1308-1311. by Zhimin Bai, Caiqiao Yin, Xunxiong Jiang, Xu Liu, Shengdong Wang posted to cobalt-rich_criusts by rabio on 2009-05-31 18:27:41 as
	SCUD: Fast structure clustering of decoys using reference state to remove overall rotation [My Copy] Journal of Computational Chemistry, Vol. 26, No. 11. (2005), pp. 1189-1192. by Hongzhi Li, Yaoqi Zhou posted to clustering rmsd by rabio on 2009-04-03 19:19:08 as
	Optimal cluster selection based on Fisher class separability measure [My Copy] American Control Conference, 2005. Proceedings of the 2005 In American Control Conference, 2005. Proceedings of the 2005 (2005), pp. 1929-1934 vol. 3. by Xudong Wang, V. L. Syrmos posted to clustering separability by rabio on 2009-03-31 15:52:38 as
	Efficient RMSD measures for the comparison of two molecular ensembles [My Copy] Proteins, Vol. 50, No. 1. (1 January 2003), pp. 26-34. by Rafael Brüschweiler posted to rmsd by rabio on 2009-03-20 17:39:51 as along with 2 people gane5h fpiazza
	Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. [My Copy] J Mol Biol, Vol. 213, No. 4. (20 June 1990), pp. 859-883. by M. J. Sippl posted to no-tag by rabio on 2008-11-24 13:57:14 as along with 7 people bicko P2324548 apostola bpb tolot27 dgront aengisch
	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 no-tag by rabio on 2008-11-24 11:42:38 as along with 7 people Gabriel439 mcbla wouterboomsma j3xucite dgront sekmi mijam
	Improving fluid intelligence with training on working memory. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 19. (13 May 2008), pp. 6829-6833. by Susanne M. Jaeggi, Martin Buschkuehl, John Jonides, Walter J. Perrig posted to brain_training cognitive by rabio on 2008-11-09 13:26:46 as along with 12 people and 1 group kerri3278 DaveCooper sen_cheng bradyandangie krokicki icitewhatilike sanchezbuelna jmaryott brockkirwan Minty shoshin mebiel VisionLab
	MaxSub: an automated measure for the assessment of protein structure prediction quality. [My Copy] Bioinformatics, Vol. 16, No. 9. (September 2000), pp. 776-785. by N. Siew, A. Elofsson, L. Rychlewski, D. Fischer posted to protein_assessment tools by rabio on 2008-11-06 13:22:45 as along with 6 people and 2 groups sebk granujilla BragilMassoud marcius dgront biehl BioinfoCIPF SGU-CIPF
	Evaluation of 3D-Jury on CASP7 models [My Copy] BMC Bioinformatics, Vol. 8 (21 August 2007), 304. by László Kaján, Leszek Rychlewski posted to tools by rabio on 2008-11-06 12:30:30 as along with 1 person mcbla
	Better decisions through science. [My Copy] Scientific American, Vol. 283, No. 4. (October 2000), pp. 82-87. by J. A. Swets, R. M. Dawes, J. Monahan posted to decision by rabio on 2008-11-06 12:16:48 as
	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 structure_prediction structure_similarity threading tools by rabio on 2008-11-05 14:27:14 as along with 6 people newton1234 mcbla karbak dgront schuylrp mijam
	Dasty2, an Ajax protein DAS client. [My Copy] Bioinformatics (Oxford, England) (11 August 2008) by Rafael C C. Jimenez, Antony F F. Quinn, Alexander Garcia, et al.Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A A. Salazar, Henning Hermjakob posted to tools by rabio on 2008-09-09 21:14:16 as along with 6 people natstreet druvus nuin niallhaslam dullhunk guhjy
	Watermarking sexually reproducing diploid organisms. [My Copy] Bioinformatics (Oxford, England) (3 July 2008) by Dominik Heider, Daniel Kessler, Angelika Barnekow posted to no-tag by rabio on 2008-08-25 18:15:33 as along with 1 person dullhunk
	mlegp: statistical analysis for computer models of biological systems using R. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 17. (1 September 2008), pp. 1966-1967. by Garrett M. Dancik, Karin S. Dorman posted to r statistics by rabio on 2008-08-25 18:11:34 as along with 3 people dah talponer guhjy
	Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions. [My Copy] Bioinformatics (Oxford, England) (30 June 2008) by David W W. Ritchie, Dima Kozakov, Sandor Vajda posted to protein_docking by rabio on 2008-08-25 16:47:23 as along with 3 people qluo kabookie reyez
	PuReD-MCL: a graph-based PubMed document clustering methodology [My Copy] Bioinformatics, Vol. 24, No. 17. (1 September 2008), pp. 1935-1941. by T. Theodosiou, N. Darzentas, L. Angelis, C. A. Ouzounis posted to clustering data_mining by rabio on 2008-08-25 16:43:41 as along with 8 people and 1 group calderonv svozil coela guhjy druvus Gaetan mitko dullhunk Bioinformatics
	Streaming XML with Jabber/XMPP [My Copy] IEEE Internet Computing, Vol. 9, No. 5. (September 2005), pp. 82-89. by Peter Saint-Andre posted to jabber xmpp by rabio on 2008-07-11 16:56:05 as
	The Quaternions with Applications to Rigid Body Dynamics; Sandia National Laboratories [My Copy] (2004) by Evangelos A. Coutsias, Louis Romero posted to quaternions by rabio on 2008-06-04 18:15:13 as
	A solution to the weighted procrustes problem in which the transformation is in agreement with the loss function [My Copy] Psychometrika, Vol. 41, No. 4. (18 December 1976), pp. 547-550. by Robert Lissitz, Peter Schönemann, James Lingoes posted to algebra rmsd svd by rabio on 2008-05-05 23:54:18 as
	A generalized solution of the orthogonal procrustes problem [My Copy] Psychometrika, Vol. 31, No. 1. (27 March 1966), pp. 1-10. by Peter Schönemann posted to algebra rmsd svd by rabio on 2008-05-05 22:23:42 as
	CDD: a Conserved Domain Database for protein classification [My Copy] Nucleic Acids Research, Vol. 33, No. Database issue. (1 January 2005), pp. D192-196. by Aron M. Bauer, John B. Anderson, Praveen F. Cherukuri, et al.Carol D. Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant posted to database by rabio on 2008-04-27 12:24:36 as along with 3 people balajis cjeans gulkur
	Dictionary of recurrent domains in protein structures [My Copy] Proteins: Structure, Function, and Genetics, Vol. 33, No. 1. (1998), pp. 88-96. by Liisa Holm, Chris Sander posted to structure_alignment structure_comparison by rabio on 2008-04-17 14:19:57 as
	ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. [My Copy] BMC Bioinformatics, Vol. 7 (April 2006), 206. by V. Sam, C. H. Tai, J. Garnier, J. F. Gibrat, B. Lee, P. J. Munson posted to structure_comparison by rabio on 2008-04-14 19:41:51 as along with 1 person karbak
	I-TASSER server for protein 3D structure prediction [My Copy] BMC Bioinformatics, Vol. 9 (23 January 2008), 40. by Yang Zhang posted to structure_prediction by rabio on 2008-04-14 19:28:05 as along with 5 people saunders chad_davis mkurc zwang mclarenv
	DaliLite workbench for protein structure comparison. [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 6. (1 June 2000), pp. 566-567. by Liisa Holm, Jong Park posted to structure_alignment structure_comparison by rabio on 2008-04-14 19:17:48 as along with 4 people jwm tomjad semin sim82
	MUSTANG: A multiple structural alignment algorithm [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 3. (2006), pp. 559-574. by Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, Arthur M. Lesk posted to multiple_sequence_alignment structure_alignment by rabio on 2008-04-08 10:33:44 as along with 4 people and 3 groups karbak ana jwm Thaverkamp structural_bioinformatics Bioinformatics Microbial-Ecology
	SuperPose: a simple server for sophisticated structural superposition. [My Copy] Nucleic Acids Research, Vol. 32, No. Web Server Issue. (1 July 2004), pp. W590-W594. by R. Maiti, G. H. Van Domselaar, H. Zhang, D. S. Wishart posted to no-tag by rabio on 2008-04-01 02:35:00 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Covariance weighted Procrustes analysis [My Copy] In LASR 2005 - Quantitative Biology, Shape Analysis, and Wavelets (4-6 July 2005), pp. 107-110. by Christopher J. Brignell, William J. Browne, Ian L. Dryden edited by S. Barber, P. D. Baxter, K. V. Mardia, R. E. Walls posted to rmsd by rabio on 2008-04-01 02:32:17 as
	Comment on 'Using quaternions to calculate RMSD' [J. Comp. Chem. 25, 1849 (2004)] [My Copy] Journal of Computational Chemistry, Vol. 26 (June 2005), pp. 1660-1662. by G. R. Kneller posted to rmsd structure_comparison by rabio on 2008-04-01 02:00:05 as
	Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller [My Copy] Journal of Computational Chemistry, Vol. 26, No. 15. (2005), pp. 1663-1665. by Evangelos A. Coutsias, Chaok Seok, Ken A. Dill posted to rmsd structure_comparison by rabio on 2008-04-01 01:49:24 as
	Using quaternions to calculate RMSD [My Copy] Journal of Computational Chemistry, Vol. 25, No. 15. (30 November 2004), pp. 1849-1857. by Evangelos A. Coutsias, Choak Seok, Ken A. Dill posted to rmsd structure_comparison by rabio on 2008-03-31 16:58:56 as along with 6 people eskay Diego_Prada BragilMassoud apaydin nachtalp dgront
	The structural alignment between two proteins: is there a unique answer? [My Copy] Protein Science : a Publication of the Protein Society, Vol. 5, No. 7. (July 1996), pp. 1325-1338. by A. Godzik posted to structure_alignment by rabio on 2008-03-31 01:41:46 as along with 3 people and 2 groups ana j3xucite Inchoate structural_bioinformatics Bioinformatics
	RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 15-21. by Tim J. P. Hubbard posted to casp rmsd by rabio on 2008-03-31 01:35:32 as along with 1 person mijam
	Matrix computations (3rd ed.) [My Copy] (1996) by Gene H. Golub, Charles F. Van Loan posted to algebra book computation numerical by rabio on 2008-03-30 22:15:25 as along with 1 person chandlerc
	Utility library for structural bioinformatics [My Copy] Bioinformatics, Vol. 24, No. 4. (15 January 2008), pp. 584-585. by Dominik Gront, Andrzej Kolinski posted to tools by rabio on 2008-03-30 22:01:59 as along with 5 people mijam mcbla chad_davis dgront Minty

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statistics	48
sequence_alignment	43
monte_carlo	28
tools	22
p-value	21
structure_prediction	21
review	20
structure_comparison	19
rmsd	16
multicanonical_ensemble	13
machine_learning	12
sequence_analysis	12
structure_alignment	12
suboptimal_alignment	12
classification	11
hmm	11
multiple_sequence_alignment	11
alignment_quality	10
decision_trees	9
force_field	9
secondary_structure	9
clustering	8
lattice_models	8
programming	8
protein_folding	8
protein_thermodynamics	8
fisher_theory	7
probabilistic_alignment	7
reduced_models	7
structure_similarity	7
threading	7
wang-landau_sampling	7
algebra	6
molecular_dynamics	6
regression	6
comparative_modeling	5
entropy_sampling	5
folding	5
phase_transition	5
postscript	5
random_forest	5
docking	4
histograms	4
homology_modeling	4
ising_model	4
knowledge-based_potentials	4
mean-field	4
measure	4
neyman-pearson_theory	4
profile	4
profile-profile_alignment	4
r	4
replica_method	4
restraints	4
sequence_profile	4
sequence_similarity	4
significance_tests	4
svd	4
astral	3
bagging	3
bayesian_analysis	3
cabs	3
contact_maps	3
fold_recognition	3
hypotheses_testing	3
metric	3
nmr	3
nonlinear_regresion	3
potencial	3
protein_assessment	3
refinement	3
sequence-structure_alignment	3
statistical_validation	3
substitution_matrices	3
water	3
1-d_structure	2
algorithms	2
bootstrap	2
charmm	2
computation	2
computing_in_medicine	2
confidence_intervals	2
conformation_serching	2
constraints	2
contacts_prediction	2
continuous_models	2
database	2
data_mining	2
decision	2
distance_geometry	2
disulphide_connections	2
dynamic_programming	2
interactions	2
manual	2
metropolis_sampling	2
multihistogram	2
numerical	2
partition_function	2
prediction_accuracy	2
profile_analysis	2
protein_docking	2
roc	2
rosetta	2
scop	2
sicho	2
simualted_aniling	2
structural_features	2
structure_fragments	2
template	2
aggregation	1
amber	1
aminoacids_distribution	1
analysis	1
bayes_factors	1
boltzmann_probability	1
book	1
brain_training	1
casp	1
cobalt-rich_criusts	1
coevolution	1
cognitive	1
comparition	1
conditioning	1
conformation	1
conformation_space_dimensionality	1
conformation_stability	1
contacts_number_prediction	1
convex	1
cox_problem	1
de_novo	1
disordered_proteins	1
distance_matrix	1
document	1
energy_function	1
energy_landscape	1
energy_minimization	1
enrtopy	1
erratum	1
evolution	1
ff99	1
fiducial_inference	1
flory_hypothesis	1
folding_mechanism	1
free_energy	1
gap_cost	1
heart_disease	1
history_of_science	1
homology_detecting	1
imbalaced_data	1
inductive_inference	1
information	1
information_theory	1
interaction_sites	1
internal_coordinates	1
inverse_folding	1
jabber	1
jeffreys_theory	1
likelihood	1
motifs	1
noe	1
oob	1
parametric_alignment	1
presentation	1
probaplistic_backtracking	1
protein_dynamics	1
protein_function_annotation	1
protein_kinetics	1
psuedo-data	1
python	1
quaternions	1
sample_reuse	1
separability	1
sequene_features	1
social_protocols	1
solvent_model	1
statistical_bias	1
statistical_inference	1
structure_class	1
svm	1
teaching	1
time_series	1
unres	1
viterbi_algorithm	1
xmpp	1

rabio's library 333 articles Export

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