vavi's protein [35 articles] Export

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	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
	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
	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
	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
	Geometric algorithms for the conformational analysis of long protein loops [My Copy] Journal of Computational Chemistry, Vol. 25, No. 7. (2004), pp. 956-967. by J. Cortés, T. Siméon, M. Remaud-Siméon, V. Tran posted to loop_analysis protein by vavi on 2006-08-14 11:00:43 as along with 1 person aqeel
	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] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D185-188. by Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, et al.Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, Baldomero 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
	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 biochimica Polonica, Vol. 51, No. 2. (2004), pp. 349-371. by Andrzej Kolinski posted to protein strutcture_prediction by vavi on 2006-07-30 09:40:22 as along with 6 people saunders 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 17 people krapnik 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
	Protein Structure Prediction: Inroads to Biology [My Copy] Molecular Cell, Vol. 20, No. 6. (22 December 2005), pp. 811-819. by Donald Petrey, Barry Honig posted to protein review strutcture_prediction by vavi on 2006-04-20 14:35:04 as along with 4 people and 2 groups pansapiens marcius penka Haggan 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
	101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem [My Copy] In RECOMB '01: Proceedings of the fifth annual international conference on Computational biology (2001), pp. 193-202. by Giuseppe Lancia, Robert Carr, Brian Walenz, Sorin Istrail posted to contact_map overlap protein structure_alignment by vavi on 2005-10-26 15:39:59 as
	Principal eigenvector of contact matrices and hydrophobicity profiles in proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 1. (2 November 2004), pp. 22-30. by Ugo Bastolla, Markus Porto, Eduardo H. Roman, Michele Vendruscolo posted to contact_matrix eigenvector protein by vavi on 2005-10-23 14:33:12 as along with 1 person mijam
	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
	Flexible docking and design. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 24 (1995), pp. 677-700. by R. Rosenfeld, S. Vajda, C. DeLisi posted to docking protein review by vavi on 2005-08-29 16:17:21 as
	Predictions of protein flexibility: First-order measures [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 4. (20 May 2004), pp. 661-668. by Julio A. Kovacs, Pablo Chacón, Ruben Abagyan posted to flexibility normal-mode-analysis prediction protein by vavi on 2005-08-28 14:37:27 as along with 3 people apaydin baaden aqeel

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

vavi's protein [35 articles] Export

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