vavi's library 100 articles Export

Ordered by to_read.

	A Branch-and-Reduce Algorithm for the Contact Overlap Problem [My Copy] by Wie Xie posted to contact_map contact_map_overlap by vavi on 2006-07-03 16:17:46 as
	PDB-based protein loop prediction: parameters for selection and methods for optimization [My Copy] Journal of Molecular Biology, Vol. 267, No. 4. (11 April 1997), pp. 975-1001. by Herman W. van Vlijmen, Martin Karplus posted to fragments library loop prediction by vavi on 2005-10-06 10:22:31 as
	Structural similarity of loops in protein families: toward the understanding of protein evolution. [My Copy] BMC Evol Biol, Vol. 5, No. 1. (3 February 2005) by A. R. Panchenko, T. Madej posted to loops similarity structure by vavi on 2005-08-24 13:50:56 as along with 1 person and 1 group Einat structural_bioinformatics
	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 ab_initio loop_prediction protein by vavi on 2006-08-28 09:32:33 as along with 2 people mijam cdeane
	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 fiser loop_modeling server structure_prediction by vavi on 2006-07-24 09:18:59 as along with 3 people mijam eckart_bindewald cdeane
	1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. [My Copy] J Comput Biol, Vol. 11, No. 1. (2004), pp. 27-52. by A. Caprara, R. Carr, S. Istrail, G. Lancia, B. Walenz posted to contact_map contact_map_similarity structure_comparison by vavi on 2006-06-27 17:06:09 as along with 2 people and 2 groups ana carlk structural_bioinformatics Bioinformatics
	Reconstruction of protein structures from a vectorial representation. [My Copy] Phys Rev Lett, Vol. 92, No. 21. (28 May 2004) by M. Porto, U. Bastolla, H. E. Roman, M. Vendruscolo posted to contact_map structure_comparison structure_prediction by vavi on 2006-06-27 15:48:24 as along with 1 person dgront
	Discrete restraint-based protein modeling and the Calpha-trace problem [My Copy] Protein Sci, Vol. 12, No. 9. (1 September 2003), pp. 2032-2046. by Mark A. Depristo, Paul I. de Bakker, Reshma P. Shetty, Tom L. Blundell posted to no-tag by vavi on 2006-06-23 13:05:22 as along with 2 people dgront medic0747
	Recent developments in structural proteomics for protein structure determination. [My Copy] Proteomics, Vol. 5, No. 8. (May 2005), pp. 2056-2068. by H. L. Liu, J. P. Hsu posted to protein_structure_prediction survey by vavi on 2006-04-20 12:30:16 as along with 3 people eravikrishnan aqeel higueruelo
	Capturing expert knowledge with argumentation: a case study in bioinformatics [My Copy] Bioinformatics, Vol. 22, No. 8. (15 April 2006), pp. 924-933. by Benjamin R. Jefferys, Lawrence A. Kelley, Marek J. Sergot, John Fox, Michael J. Sternberg posted to argumentation bioinformatics expert_knowledge by vavi on 2006-04-02 12:18:53 as along with 3 people and 2 groups mdimmic marcius eweaver BioinfoCIPF SGU-CIPF
	Ab initio modeling of small, medium, and large loops in proteins [My Copy] Peptide Science, Vol. 60, No. 2. (6 July 2001), pp. 153-168. by Stan Galaktionov, Gregory V. Nikiforovich, Garland R. Marshall posted to ab_initio contact_map loop_prediction protein by vavi on 2005-11-07 15:54:00 as
	Algorithmic Aspects of Protein Structure Similarity [My Copy] In FOCS '99: Proceedings of the 40th Annual Symposium on Foundations of Computer Science (1999) by Deborah Goldman, Christos H. Papadimitriou, Sorin Istrail posted to algorithm protein structure_similarity by vavi on 2005-10-23 14:32:30 as
	Protein loop structure prediction with flexible stem geometries. [My Copy] Proteins (12 October 2005) by M Mönnigmann, C A A. Floudas posted to loop protein structure_prediction by vavi on 2005-10-20 13:19:50 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Network Analysis of Protein Structures Identifies Functional Residues [My Copy] Journal of Molecular Biology, Vol. 344, No. 4. (03 December 2004), pp. 1135-1146. by Gil Amitai, Arye Shemesh, Einat Sitbon, et al.Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski posted to closeness residue_property by vavi on 2005-10-16 15:39:06 as along with 8 people and 1 group Diego_Prada chrn bicko Einat amitai sriram_s massivemayhem siebertm structural_bioinformatics
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to prediction structure by vavi on 2005-09-19 08:29:33 as along with 11 people and 4 groups ucbcjbm paddydu kgutwin BragilMassoud ana barry thaliana jwm marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. [My Copy] Protein Sci, Vol. 1, No. 2. (February 1992), pp. 216-226. by J. Overington, D. Donnelly, M. S. Johnson, A. Sali, T. L. Blundell posted to acid amino matrix substitution by vavi on 2005-08-16 12:52:18 as along with 5 people and 1 group gjuggler bicko Einat massivemayhem medic0747 structural_bioinformatics
	EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (10 January 2005) by J. C. Gelly, L. Chiche, J. Gracy posted to matrix prediction structure substitution by vavi on 2005-08-16 12:21:49 as along with 1 person rabio
	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 protein review structure_prediction by vavi on 2006-11-29 14:59:03 as along with 18 people and 3 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain [My Copy] Protein Sci, Vol. 13, No. 3. (1 March 2004), pp. 608-616. by Christian Blouin, Davin Butt, Andrew J. Roger posted to no-tag by vavi on 2006-10-11 18:04:25 as
	High-throughput computational and experimental techniques in structural genomics. [My Copy] Genome Res, Vol. 14, No. 10B. (October 2004), pp. 2145-2154. by M. R. Chance, A. Fiser, A. Sali, et al.U. Pieper, N. Eswar, G. Xu, J. E. Fajardo, T. Radhakannan, N. Marinkovic posted to no-tag by vavi on 2006-10-11 16:58:12 as along with 2 people flbarroso dgront
	Evolution and physics in comparative protein structure modeling. [My Copy] Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 413-421. by A. Fiser, M. Feig, C. L. Brooks, A. Sali posted to comparative_modeling structure_prediction by vavi on 2006-10-11 16:51:26 as along with 2 people and 2 groups barry insectopalo structural_bioinformatics Bioinformatics
	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 machine_learning by vavi on 2006-10-02 20:56:57 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 dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos cdeane haiyeong AbnerCYH isimpson guhjy nherveg Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
	Geometry-based flexible and symmetric protein docking. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 224-231. by D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, H. J. Wolfson posted to docking flexdock protein by vavi on 2006-09-13 09:06:46 as along with 2 people and 2 groups bicko marcius BioinfoCIPF SGU-CIPF
	Approximate protein structural alignment in polynomial time. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12201-12206. by R. Kolodny, N. Linial posted to protein structure_alignment by vavi on 2006-08-15 14:57:20 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	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_map contact_map_prediction protein by vavi on 2006-08-15 14:20:02 as along with 2 people mcbla babakap
	A contact map matching approach to protein structure similarity analysis. [My Copy] Genet Mol Res, Vol. 5, No. 2. (2006), pp. 284-308. by R. C. de Melo, C. E. Lopes, F. A. Fernandes, et al.C. H. da Silveira, M. M. Santoro, R. L. Carceroni, W. Meira, A. d. e. . A. Araújo posted to contact_map image_processing protein_similarity by vavi on 2006-08-14 15:10:44 as along with 2 people dgront mijam
	A combined optimization method for solving the inverse kinematics problems of mechanical manipulators [My Copy] Robotics and Automation, IEEE Transactions on, Vol. 7, No. 4. (1991), pp. 489-499. by L. C. T. Wang, C. C. Chen posted to inverse_kinematics robotics by vavi on 2006-08-14 10:34:46 as along with 1 person and 1 group jimesh Inverse_Kinematics
	LGA: A method for finding 3D similarities in protein structures. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3370-3374. by A. Zemla posted to contact_map protein structure_comparison by vavi on 2006-08-13 14:28:27 as along with 4 people and 2 groups dfdong karbak ana analogAI structural_bioinformatics Bioinformatics
	Model for haptoglobin heavy chain based upon structural homology. [My Copy] Proc Natl Acad Sci U S A, Vol. 77, No. 6. (June 1980), pp. 3393-3397. by J. Greer posted to knowledge_based loop_modeling protein by vavi on 2006-08-06 13:21:44 as
	Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures. [My Copy] Pac Symp Biocomput (1996), pp. 570-589. by S. D. Rufino, L. E. Donate, L. Canard, T. L. Blundell posted to classification loop_modeling protein by vavi on 2006-08-06 09:11:06 as along with 1 person medic0747
	ArchDB: automated protein loop classification as a tool for structural genomics. [My Copy] Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004) by J. Espadaler, N. Fernandez-Fuentes, A. Hermoso, et al.E. Querol, F. X. Aviles, M. J. Sternberg, B. Oliva posted to classification loop protein by vavi on 2006-08-06 09:06:23 as along with 2 people mijam baldo
	CODA: a combined algorithm for predicting the structurally variable regions of protein models. [My Copy] Protein Sci, Vol. 10, No. 3. (March 2001), pp. 599-612. by C. M. Deane, T. L. Blundell posted to hybrid protein structure_prediction by vavi on 2006-08-05 13:07:33 as along with 2 people medic0747 cdeane
	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions [My Copy] Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 209-225. by K. Simons posted to comparative_modeling protein strutcture_prediction by vavi on 2006-07-31 13:48:24 as along with 12 people and 2 groups chemrahul82 paddydu Diego_Prada reyez guxiyou ana jwm wouterboomsma j3xucite hmk mijam joule structural_bioinformatics Bioinformatics
	A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. [My Copy] Proteins, Vol. 40, No. 1. (1 July 2000), pp. 135-144. by C. M. Deane, T. L. Blundell posted to loop_modeling protein by vavi on 2006-07-31 12:27:08 as along with 3 people thamelry medic0747 cdeane
	A divide and conquer approach to fast loop modeling [My Copy] Protein Eng., Vol. 15, No. 4. (1 April 2002), pp. 279-286. by Silvio C. Tosatto, Eckart Bindewald, Jurgen Hesser, Reinhard Manner posted to ab_initio loop_modeling protein by vavi on 2006-07-31 10:31:02 as
	Cyclic coordinate descent: A robotics algorithm for protein loop closure. [My Copy] Protein Sci, Vol. 12, No. 5. (May 2003), pp. 963-972. by A. A. Canutescu, R. L. Dunbrack posted to kinematics loop_modeling protein by vavi on 2006-07-31 10:26:25 as along with 4 people and 1 group yongzhao j3xucite dgront mijam TSRI_MGL
	Prediction of loop geometries using a generalized born model of solvation effects [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 173-183. by Chaya S. Rapp, Richard A. Friesner posted to ab_initio molecular_dynamics monte_carlo protein structure_prediction by vavi on 2006-07-31 09:23:54 as
	Conformational sampling using high-temperature molecular dynamics. [My Copy] Biopolymers, Vol. 29, No. 14. (December 1990), pp. 1847-1862. by R. E. Bruccoleri, M. Karplus posted to loop_prediction molecular_dynamics protein by vavi on 2006-07-31 09:16:32 as
	Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. [My Copy] Proteins, Vol. 46, No. 1. (1 January 2002), pp. 128-146. by Y. Liu, D. L. Beveridge posted to ab_initio molecular_dynamics monte_carlo protein simulated_annealing structure_prediction by vavi on 2006-07-31 09:00:25 as along with 1 person flbarroso
	Structural prediction of peptides bound to MHC class I. [My Copy] J Mol Biol, Vol. 356, No. 2. (17 February 2006), pp. 521-546. by T. Fagerberg, J. C. Cerottini, O. Michielin posted to molecular_dynamics protein simulated_annealing structure_prediction by vavi on 2006-07-31 08:54:09 as
	Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins [My Copy] Biopolymers, Vol. 32, No. 1. (1992), pp. 33-43. by Junichi Higo, Vincent Collura, Jean Garnier posted to loop_prediction simulated_annealing by vavi on 2006-07-30 14:22:44 as
	The loop problem in proteins: A monte carlo simulated annealing approach [My Copy] Biopolymers, Vol. 33, No. 8. (1993), pp. 1271-1286. by Louis Carlacci, Walter S. Englander posted to loop_prediction monte_carlo protein simulated_annealing by vavi on 2006-07-30 14:18:24 as
	ModLoop: automated modeling of loops in protein structures. [My Copy] Bioinformatics, Vol. 19, No. 18. (12 December 2003), pp. 2500-2501. by A. Fiser, A. Sali posted to loop_prediction protein server by vavi on 2006-07-30 13:17:51 as along with 1 person tji
	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 protein strutcture_prediction by vavi on 2006-07-30 09:40:22 as along with 5 people dgront rabio sekmi mijam mcbla
	Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (28 June 2005), 159. by Wouter Boomsma, Thomas Hamelryck posted to loop_modeling protein by vavi on 2006-07-25 16:52:24 as along with 4 people mijam cdeane pansapiens wouterboomsma
	Ab initio protein structure prediction: progress and prospects. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 30 (2001), pp. 173-189. by R. Bonneau, D. Baker posted to ab_initio protein review structure_prediction by vavi on 2006-07-25 14:29:29 as along with 2 people flbarroso dgront
	Tools for comparative protein structure modeling and analysis. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3375-3380. by N. Eswar, B. John, N. Mirkovic, et al.A. Fiser, V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Marti-Renom, M. S. Madhusudhan, B. Yerkovich, A. Sali posted to comparative_modeling protein strutcture_prediction by vavi on 2006-07-25 14:23:56 as along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
	Comparative protein modelling by satisfaction of spatial restraints. [My Copy] Journal of molecular biology, Vol. 234, No. 3. (5 December 1993), pp. 779-815. by A. Sali, T. L. Blundell posted to protein structure_prediction by vavi on 2006-07-25 13:44:57 as along with 16 people bmduggan pjcite newton1234 viktor21614 mijam dimka bicko chad_davis ttjoseph skhadar dgront rabio massivemayhem medic0747 sebk granujilla
	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 database fragments protein by vavi on 2006-07-25 11:21:49 as along with 3 people iakes cdeane saunders
	A composite score for predicting errors in protein structure models [My Copy] Protein Science, Vol. 15, No. 7. (July 2006), pp. 1653-1666. by David Eramian, Min-yi Shen, Damien Devos, Francisco Melo, Andrej Sali, Marc A. Marti-Renom posted to protein_structure svm by vavi on 2006-07-25 10:39:39 as along with 5 people rabio dimka wouterboomsma mijam j3xucite

Note: You may cite this page as: http://www.citeulike.org/user/vavi/order/to_read

Result page: 1 2 Next

protein	35
contact_map	16
structure_prediction	15
prediction	14
loop	9
loop_modeling	8
review	7
ab_initio	6
loop_prediction	6
fragments	5
structure	5
docking	4
molecular_dynamics	4
simulated_annealing	4
structure_comparison	4
strutcture_prediction	4
comparative_modeling	3
contact_maps	3
database	3
loops	3
monte_carlo	3
sequence_alignment	3
structure_alignment	3
bioinformatics	2
classification	2
contact_map_prediction	2
contact_map_similarity	2
energy	2
library	2
matrix	2
programming	2
protein_structure	2
sequence	2
server	2
similarity	2
structure_similarity	2
strucure_prediction	2
substitution	2
acid	1
algorithm	1
all-atom	1
amino	1
angles	1
argumentation	1
baker	1
boston	1
closeness	1
contact_map_overlap	1
contact_maps_use	1
contact_matrix	1
context	1
drug-companies	1
eigenvector	1
engine	1
expert_knowledge	1
fiser	1
flexdock	1
flexibility	1
function	1
google	1
hybrid	1
image_processing	1
inverse_kinematics	1
kinematics	1
knowledge_based	1
loop_analysis	1
machine_learning	1
main-chain	1
modeling	1
motivation	1
normal-mode-analysis	1
overlap	1
packing	1
pdb	1
protein_similarity	1
protein_structure_prediction	1
ranking	1
residue_property	1
robotics	1
rosetta	1
scoring	1
search	1
side-chain	1
structural_genomics	1
substitution_matrix	1
supersecondary_library	1
survey	1
svm	1
visualization	1
volume	1

vavi's library 100 articles Export

vavi's tags