Group: Structural Biology Group TorVergata - with tag docking [61 articles] Export

Recent papers posted by members of the Structural Biology Group TorVergata group with tag docking

	Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti, Miriam Sgobba posted to poisson_boltzman docking by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-10-27 22:07:14 as along with 1 person sobolevnrm
	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2743-2744. by T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, C. Micheletti posted to domain_movement docking by oteri to the group Structural Biology Group TorVergata on 2009-10-21 11:44:43 as along with 1 person apaydin
	Synthesis of new modified truncated peptides and inhibition of glycogen phosphorylase. [My Copy] Journal of peptide science : an official publication of the European Peptide Society, Vol. 15, No. 6. (June 2009), pp. 442-450. by Stephanie S. Schweiker, Wendy A. Loughlin, Christopher L. Brown, Gregory K. Pierens posted to peptide docking by oteri to the group Structural Biology Group TorVergata on 2009-10-06 16:15:43 as
	Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A [My Copy] PLoS ONE, Vol. 2, No. 8. (22 August 2007), e761. by Jing Tang, Jewn G. Park, Charles B. Millard, James J. Schmidt, Yuan-Ping Pang posted to znua docking by oteri to the group Structural Biology Group TorVergata on 2009-09-17 18:40:07 as along with 1 group znu
	GARD: A Generally Applicable Replacement for RMSD [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1889-1900. by J. Christian Baber, David C. Thompson, Jason B. Cross, Christine Humblet posted to modeling docking by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-09-15 12:10:11 as along with 3 people nickolay zimbo1 reyez
	Docking Studies on DNA-Ligand Interactions: Building and Application of a Protocol To Identify the Binding Mode [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1925-1935. by Clarisse G. Ricci, Paulo A. Netz posted to molecular_dynamics docking dna by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-09-15 12:06:49 as
	Mining Molecular Fragments: Finding Relevant Substructures of Molecules [My Copy] posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-04-13 14:41:35 as along with 1 person klexa
	ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by Meytal Landau, Itay Mayrose, Yossi Rosenberg, et al.Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-04-03 17:06:29 as along with 8 people pablocarb tomjad klexa shacko ramiro2k chrn sriram_s bicko
	ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 163-164. by F. Glaser, T. Pupko, I. Paz, et al.R. E. Bell, D. Bechor-Shental, E. Martz, N. Ben-Tal posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-04-03 17:05:47 as along with 4 people tomjad chrn bicko siebertm
	Steps towards flexible docking: Modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators’ sequences [My Copy] The Journal of Steroid Biochemistry and Molecular Biology, Vol. 103, No. 3-5. (March 2007), pp. 357-360. by M. Kurcinski, A. Kolinski posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-04-03 16:45:47 as along with 3 people rabio klexa mkurc
	AutoGrow: a novel algorithm for protein inhibitor design. [My Copy] Chemical biology & drug design, Vol. 73, No. 2. (February 2009), pp. 168-178. by Jacob D. Durrant, Rommie E. Amaro, J. Andrew McCammon posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-03-15 22:48:27 as along with 1 person and 1 group klexa LOX-1 Receptor
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-02-16 16:38:50 as along with 5 people and 1 group pansapiens klexa abovell sobolevnrm middledomain baker-group
	Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin [My Copy] Proteins: Structure, Function, and Genetics, Vol. 40, No. 2. (2000), pp. 258-289. by Collin M. Stultz, Martin Karplus posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-02-13 14:05:32 as
	An automated method for dynamic ligand design. [My Copy] Proteins, Vol. 23, No. 4. (December 1995), pp. 472-490. by A. Miranker, M. Karplus posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-02-13 14:05:14 as along with 2 people klexa dfgreen
	FlexNovo: Structure-Based Searching in Large Fragment Spaces [My Copy] posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-02-13 14:04:51 as along with 1 person klexa
	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1549-1562. by Guosheng Wu, Daniel H. Robertson, Charles L. Brooks, Michal Vieth posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-02-03 18:02:34 as along with 5 people oceanwind apostola papatonyhill mmuecke msuarezdiez
	A review of protein-small molecule docking methods. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-02-03 17:58:47 as along with 6 people and 4 groups klexa csrocha marcius sangeetha schlauchi massivemayhem Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. [My Copy] Journal of computer-aided molecular design, Vol. 21, No. 5. (27 May 2007), pp. 281-306. by A. N. Jain posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-02-03 17:48:06 as along with 3 people and 2 groups vpenelle BragilMassoud sangeetha Bioinformatics insilicodrug
	Rational design of affinity peptide ligand by flexible docking simulation [My Copy] Journal of Chromatography A, Vol. 1146, No. 1. (30 March 2007), pp. 41-50. by Fu-Feng Liu, Tao Wang, Xiao-Yan Dong, Yan Sun posted to docking protein-peptide_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-03 17:34:18 as along with 1 person carlescorbi
	Peptide docking using dynamic programming [My Copy] Journal of Computational Chemistry, Vol. 17, No. 4. (1996), pp. 418-428. by Kamalakar Gulukota, Sandor Vajda, Charles Delisi posted to docking protein-peptide_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-03 16:39:28 as along with 1 person ima
	Flexible Peptide-Protein Docking Employing PSO@Autodock [My Copy] posted to docking protein-peptide_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-03 16:07:09 as
	An Evolutionary Approach for Structure-based Design of Natural and Non-natural Peptidic Ligands [My Copy] Combinatorial Chemistry & High Throughput Screening (December 2001), pp. 661-673. by N. Budin, S. Ahmed, N. Majeux, A. Caflisch posted to docking protein-peptide_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-03 14:27:11 as
	ClusPro: Performance in CAPRI rounds 6-11 and the new server [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. 4. (2007), pp. 781-785. by Stephen R. Comeau, Dima Kozakov, Ryan Brenke, Yang Shen, Dmitri Beglov, Sandor Vajda posted to docking protein-protein_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-02 16:25:27 as
	Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 245-251. by C. J. Camacho posted to docking protein-protein_dock by oteri to the group Structural Biology Group TorVergata on 2009-02-02 16:22:42 as along with 1 person and 1 group qzhang TSRI_MGL
	Automated molecular design: A new fragment-joining algorithm [My Copy] Journal of Computer-Aided Molecular Design, Vol. 8, No. 3. (1 June 1994), pp. 283-298. by Andrew R. Leach, Simon R. Kilvington posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-02-01 19:43:48 as
	The Levelwise Version Space Algorithm and its Application to Molecular Fragment Finding [My Copy] posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-02-01 19:39:52 as
	Novel Indazole Non-Nucleoside Reverse Transcriptase Inhibitors Using Molecular Hybridization Based on Crystallographic Overlays† [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Lyn H. Jones, Gill Allan, Oscar Barba, et al.Catherine Burt, Romuald Corbau, Thomas Dupont, Thorsten Knöchel, Steve Irving, Donald S. Middleton, Charles E. Mowbray, Manos Perros, Heather Ringrose, Nigel A. Swain, Robert Webster, Mike Westby, Chris Phillips posted to docking drug_design by oteri to the group Structural Biology Group TorVergata on 2009-01-30 10:44:48 as
	Discovery of (2S,4R)-1-(2-Aminoacetyl)-4-benzamidopyrrolidine-2-carboxylic Acid Hydrochloride (GAP-134)13, an Orally Active Small Molecule Gap-Junction Modifier for the Treatment of Atrial Fibrillation [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by John A. Butera, Bjarne D. Larsen, James K. Hennan, et al.Edward Kerns, Li Di, Asaf Alimardanov, Robert E. Swillo, Gwen A. Morgan, Kun Liu, Qiang Wang, Eric I. Rossman, Rayomand Unwalla, Leonard Mcdonald, Christine Huselton, Jørgen S. Petersen posted to docking drug_design by oteri to the group Structural Biology Group TorVergata on 2009-01-30 10:41:06 as
	Derivatives of 5-Nitro-furan-2-carboxylic Acid Carbamoylmethyl Ester Inhibit RNase H Activity Associated with HIV-1 Reverse Transcriptase [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Hideyoshi Fuji, Emiko Urano, Yuko Futahashi, et al.Makiko Hamatake, Junko Tatsumi, Tyuji Hoshino, Yuko Morikawa, Naoki Yamamoto, Jun Komano posted to docking drug_design by oteri to the group Structural Biology Group TorVergata on 2009-01-30 10:39:35 as
	Fragment molecular orbital method: application to polypeptides [My Copy] Chemical Physics Letters (March 2000), pp. 614-618. by T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi, K. Kitaura posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-28 10:27:49 as
	Searching Fragment Spaces with Feature Trees [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Uta Lessel, Bernd Wellenzohn, Markus Lilienthal, Holger Claussen posted to algorithm docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:24:03 as along with 2 people zimbo1 reyez
	Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sebastian G. Rohrer, Knut Baumann posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:22:07 as along with 1 person sschurer
	Evaluating Docking Methods for Prediction of Binding Affinities of Small Molecules to the G Protein βγ Subunits [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Min-Sun Park, Axel L. Dessal, Alan V. Smrcka, Harry A. Stern posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:20:56 as along with 1 person carlosjavierna
	De Novo Drug Design Using Multiobjective Evolutionary Graphs [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Christos A. Nicolaou, Joannis Apostolakis, Costas S. Pattichis posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:19:14 as along with 2 people sschurer carlosjavierna
	Guided Docking Approaches to Structure-Based Design and Screening [My Copy] Current Topics in Medicinal Chemistry, Vol. 4, No. 7. (March 2004), pp. 687-700. by X. Fradera, J. Mestres posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:14:25 as along with 3 people and 2 groups LamBras dgruiz sangeetha Bioinformatics insilicodrug
	Recent progress and future directions in protein-protein docking. [My Copy] Current protein & peptide science, Vol. 9, No. 1. (February 2008), pp. 1-15. by D. W. Ritchie posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:07:52 as along with 1 person flbarroso
	[Receptor-ligand docking simulation for membrane proteins] [My Copy] Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan, Vol. 127, No. 1. (January 2007), pp. 123-131. by T. Hirokawa posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-01-27 23:07:15 as
	QXP: powerful, rapid computer algorithms for structure-based drug design. [My Copy] J Comput Aided Mol Des, Vol. 11, No. 4. (July 1997), pp. 333-344. by C. McMartin, R. S. Bohacek posted to docking drug_design by oteri to the group Structural Biology Group TorVergata on 2009-01-27 14:25:21 as along with 2 people flbarroso BragilMassoud
	A semiempirical free energy force field with charge-based desolvation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (1 February 2007), pp. 1145-1152. by Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 14:24:39 as along with 6 people trishul nickolay joule IrinaMoreira BragilMassoud carlescorbi
	A model binding site for testing scoring functions in molecular docking. [My Copy] J Mol Biol, Vol. 322, No. 2. (13 September 2002), pp. 339-355. by B. Q. Wei, W. A. Baase, L. H. Weaver, B. W. Matthews, B. K. Shoichet posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 14:21:33 as
	Physics-based methods for studying protein-ligand interactions. [My Copy] Curr Opin Drug Discov Devel, Vol. 10, No. 3. (May 2007), pp. 325-331. by N. Huang, M. P. Jacobson posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 14:16:03 as along with 3 people flbarroso superpyrin higueruelo
	Molecular modeling of hydration in drug design. [My Copy] Current opinion in drug discovery & development, Vol. 10, No. 3. (May 2007), pp. 275-280. by R. L. Mancera posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 14:09:01 as along with 2 people flbarroso superpyrin
	FE: efficient molecular docking considering protein structure variations [My Copy] Journal of Molecular Biology, Vol. 308, No. 2. (27 April 2001), pp. 377-395. by Holger Clau[ss]en, Christian Buning, Matthias Rarey, Thomas Lengauer posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-01-27 13:50:23 as along with 5 people LamBras apaydin blackbart kazemi carlk
	Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 2. (9 November 2007), pp. 399-421. by Sheng-You Huang, Xiaoqin Zou posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 13:45:31 as along with 8 people and 1 group nickolay AliceWang BragilMassoud bicko yongzhao kazemi hmk LamBras TSRI_MGL
	Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (15 November 2001), pp. 34-40. by Fredrik österberg, Garrett M. Morris, Michel F. Sanner, Arthur J. Olson, David S. Goodsell posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-27 13:44:16 as along with 2 people and 1 group yongzhao peprovy TSRI_MGL
	Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 2. (22 January 2009), pp. 569-573. by Stefania Ferro, Laura De Luca, Maria L. Barreca, et al.Nunzio Iraci, Sara De Grazia, Frauke Christ, Myriam Witvrouw, Zeger Debyser, Alba Chimirri posted to docking drug_design by oteri to the group Structural Biology Group TorVergata on 2009-01-26 11:06:23 as
	Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods. [My Copy] Curr Med Chem, Vol. 11, No. 23. (December 2004), pp. 3093-3118. by P. Cozzini, M. Fornabaio, A. Marabotti, D. J. Abraham, G. E. Kellogg, A. Mozzarelli posted to docking by oteri to the group Structural Biology Group TorVergata on 2009-01-15 10:39:16 as along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
	DNA–psoralens molecular recognition using molecular dynamics [My Copy] Il Farmaco, Vol. 54, No. 4. (30 April 1999), pp. 202-212. by R. Boggia posted to dna docking molecular_dynamics psoralens by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 14:47:41 as
	Biophysical Journal - Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics [My Copy] posted to docking docking_prog by oteri to the group Structural Biology Group TorVergata on 2009-01-13 18:18:29 as
	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. [My Copy] J Comput Aided Mol Des (15 January 2008) by Rommie E. Amaro, Riccardo Baron, J A. McCammon posted to cluster_analysis docking by oteri to the group Structural Biology Group TorVergata on 2009-01-10 17:27:27 as along with 6 people and 1 group karinaecomp jmccammon rbaron higueruelo kazemi LamBras McCammon

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protein	156
review	108
screening	107
structure	96
drug	81
ligand	68
scoring	66
binding	56
flexibility	46
algorithms	40
protein-protein	34
drug_design	33
docking_prog	32
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ppi	29
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algorithm	26
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cheminformatics	7
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ga	7
library	7
md_simulation	7

Group: Structural Biology Group TorVergata

Group: Structural Biology Group TorVergata - with tag docking [61 articles] Export

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