oteri's watchlist [151 articles] Export

Recent papers matching oteri's watchlist criteria

	MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by D. T. Chang, Y. J. Oyang, J. H. Lin posted to docking by oteri to the group TSRI_MGL on 2008-12-02 08:33:58 as
	FLIPDock: Docking flexible ligands into flexible receptors [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (23 May 2007), pp. 726-737. by Yong Zhao, Michel F. Sanner posted to side_chain rotamer_lib induced_fit flex docking cross_docking by yongzhao to the group TSRI_MGL on 2007-07-27 17:59:04 as along with 7 people npt11tpn fl karinaecomp BragilMassoud kazemi somak LamBras
	Side-chain flexibility in proteins upon ligand binding [My Copy] Proteins: Structure, Function, and Genetics, Vol. 39, No. 3. (2000), pp. 261-268. by Rafael Najmanovich, Josef Kuttner, Vladimir Sobolev, Marvin Edelman posted to side_chain by yongzhao to the group TSRI_MGL on 2007-06-29 23:54:07 as along with 3 people fl kazemi LamBras
	Pharmacophore Modeling and Three Dimensional Database Searching for Drug Design Using Catalyst: Recent Advances [My Copy] pp. 2991-3005. by Osman Guner posted to library screening by yongzhao to the group TSRI_MGL on 2007-03-05 21:16:33 as
	Trends in Virtual Combinatorial Library Design [My Copy] pp. 2095-2101. by G. Schneider posted to library screening by yongzhao to the group TSRI_MGL on 2007-03-05 21:14:52 as along with 1 person LamBras
	Can Conformational Change Be Described by Only a Few Normal Modes? [My Copy] Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593. by Paula Petrone, Vijay S. Pande posted to normal_mode_analysis by yongzhao to the group TSRI_MGL on 2007-01-29 00:11:25 as along with 12 people and 6 groups ahmetbakan csrocha BragilMassoud barry dimka aqeel shuns xdeupi choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics LabCompMed
	Protein flexibility and drug design: how to hit a moving target [My Copy] Current Opinion in Chemical Biology, Vol. 6, No. 4. (1 August 2002), pp. 447-452. by Heather A. Carlson posted to review flex by yongzhao to the group TSRI_MGL on 2007-01-22 19:39:07 as along with 1 person LamBras
	Conformational changes studied by cryo-electron microscopy. [My Copy] Nat Struct Biol, Vol. 7, No. 9. (September 2000), pp. 711-714. by H. R. Saibil posted to cryoem by yongzhao to the group TSRI_MGL on 2007-01-17 18:39:26 as along with 2 people aqeel dgront
	NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps [My Copy] Acta Crystallographica Section D: Biological Crystallography, Vol. 62, No. 9. (01 September 2006), pp. 1098-1100. by Suhre, K., Navaza, J., Sanejouand, -H posted to cryoem by yongzhao to the group TSRI_MGL on 2007-01-17 18:35:28 as along with 4 people martainn dawnsong apaydin aqeel
	Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM [My Copy] Journal of Structural Biology, Vol. 147, No. 3. (September 2004), pp. 315-326. by Florence Tama, Osamu Miyashita, Charles L. Brooks III posted to cryoem by yongzhao to the group TSRI_MGL on 2007-01-17 18:30:17 as along with 1 person aqeel
	Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. [My Copy] Biophys J, Vol. 88, No. 2. (February 2005), pp. 818-827. by K. Hinsen, N. Reuter, J. Navaza, D. L. Stokes, J. J. Lacapère posted to cryoem by yongzhao to the group TSRI_MGL on 2007-01-17 18:23:56 as along with 1 person aqeel
	Critical assessment of the automated AutoDock as a new docking tool for virtual screening. [My Copy] Proteins (20 September 2006) by Hwangseo Park, Jinuk Lee, Sangyoub Lee posted to screening by yongzhao to the group TSRI_MGL on 2007-01-15 20:54:23 as along with 3 people BragilMassoud dgruiz insilico
	Progressive Docking: A Hybrid QSAR/Docking Approach for Accelerating In Silico High Throughput Screening. [My Copy] J Med Chem, Vol. 49, No. 25. (14 December 2006), pp. 7466-7478. by Artem Cherkasov, Fuqiang Ban, Yvonne Li, Magid Fallahi, Geoffrey L. Hammond posted to screening qsar docking by yongzhao to the group TSRI_MGL on 2007-01-11 19:25:04 as along with 1 person BragilMassoud
	Development and validation of a modular, extensible docking program: DOCK 5. [My Copy] J Comput Aided Mol Des (6 December 2006) by Demetri T. Moustakas, P T. Lang, Scott Pegg, et al.Eric Pettersen, Irwin D. Kuntz, Natasja Brooijmans, Robert C. Rizzo posted to docking_design by yongzhao to the group TSRI_MGL on 2007-01-11 19:15:50 as along with 2 people BragilMassoud schlauchi
	Gradient tabu search. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 601-611. by S. Stepanenko, B. Engels posted to search docking_design by yongzhao to the group TSRI_MGL on 2007-01-10 00:14:24 as along with 1 person BragilMassoud
	Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 580-592. by Z. Zhou, M. Bates, J. D. Madura posted to induced_fit by yongzhao to the group TSRI_MGL on 2007-01-08 17:58:14 as
	Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility [My Copy] Journal of Computational Chemistry, Vol. 23, No. 16. (2002), pp. 1656-1670. by Visvaldas Kairys, Michael K. Gilson posted to cross_docking docking ga search by yongzhao to the group TSRI_MGL on 2007-01-03 21:51:37 as along with 3 people and 1 group blackbart kazemi arlam Chang group
	A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. [My Copy] J Mol Graph Model, Vol. 18, No. 3. (June 2000) by H. B. Broughton posted to docking flex induced_fit screening by yongzhao to the group TSRI_MGL on 2007-01-03 21:43:02 as along with 2 people kazemi LamBras
	Mining the NCI antiviral compounds for HIV-1 integrase inhibitors [My Copy] Bioorganic & Medicinal Chemistry, Vol. 14, No. 11. (1 June 2006), pp. 3785-3792. by Jinxia Deng, James A. Kelley, Joseph J. Barchi, et al.Tino Sanchez, Raveendra Dayam, Yves Pommier, Nouri Neamati posted to hivin by yongzhao to the group TSRI_MGL on 2006-12-11 19:08:17 as
	HIV-1 integrase inhibitors: a decade of research and two drugs in clinical trial. [My Copy] Curr Top Med Chem, Vol. 4, No. 10. (2004), pp. 1059-1077. by A. A. Johnson, C. Marchand, Y. Pommier posted to hivin by yongzhao to the group TSRI_MGL on 2006-12-11 18:37:56 as
	Application of CoMFA and CoMSIA 3D-QSAR and Docking Studies in Optimization of Mercaptobenzenesulfonamides as HIV-1 Integrase Inhibitors [My Copy] J. Med. Chem., Vol. 47, No. 2. (15 January 2004), pp. 385-399. by C. L. Kuo, H. Assefa, S. Kamath, et al.Z. Brzozowski, J. Slawinski, F. Saczewski, J. K. Buolamwini, N. Neamati posted to hiv hivin potential_app by yongzhao to the group TSRI_MGL on 2006-12-11 18:30:24 as
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to potential_app loop by yongzhao to the group TSRI_MGL on 2006-11-21 19:00:57 as along with 10 people aqeel reyez BragilMassoud dgruiz radestock lna choonpeng weisblum higueruelo nickolay
	Patented HIV-1 Integrase Inhibitors (1998-2005) [My Copy] Recent Patents on Anti-Infective Drug Discovery, Vol. 1, No. 1. (January 2006), pp. 1-15. by Philippe Cotelle posted to hivin by yongzhao to the group TSRI_MGL on 2006-11-15 23:48:27 as
	ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (13 September 2006), pp. 538-548. by Jens Meiler, David Baker posted to docking_design side_chain by yongzhao to the group TSRI_MGL on 2006-11-08 23:55:35 as along with 4 people mijam BragilMassoud kuhn jwm
	Protein-ligand docking: Current status and future challenges. [My Copy] Proteins (21 July 2006) by Sérgio Filipe F. Sousa, Pedro Alexandrino A. Fernandes, Maria João J. Ramos posted to autodock docking by yongzhao to the group TSRI_MGL on 2006-11-07 19:07:30 as along with 10 people and 1 group flbarroso ramensky BragilMassoud peprovy kazemi sergio_fms carlescorbi robert boris_aguilar qaiser_fatmi Chang group
	Novel transition metal multiple bonding-myth or reality? - A computational study of boryl complexes [My Copy] by T. R. Cundari posted to mine by yongzhao to the group TSRI_MGL on 2006-11-06 23:38:20 as
	Design of a Propane Ammoxidation Catalyst Using Artificial Neural Networks and Genetic Algorithms [My Copy] Ind. Eng. Chem. Res., Vol. 40, No. 23. (14 November 2001), pp. 5475-5480. by T. Cundari, J. Deng, Y. Zhao posted to mine by yongzhao to the group TSRI_MGL on 2006-11-06 23:32:48 as
	Novel transition metal multiple bonding--myth or reality?: A computational study of boryl complexes [My Copy] Inorganica Chimica Acta In Protagonists in Chemistry: Richard R. Schrock, Vol. 345 (10 March 2003), pp. 70-80. by Thomas R. Cundari, Yong Zhao posted to mine by yongzhao to the group TSRI_MGL on 2006-11-06 23:32:06 as
	Hierarchical and multi-resolution representation of protein flexibility. [My Copy] Bioinformatics (18 September 2006) by Yong Zhao, Daniel Stoffler, Michel Sanner posted to mine by yongzhao to the group TSRI_MGL on 2006-11-06 23:26:57 as along with 4 people BragilMassoud dgruiz kazemi LamBras
	ONIOM study of the active species in Pd-phosphine catalyzed coupling reactions [My Copy] pp. 121-129. by T. R. Cundari posted to mine by yongzhao to the group TSRI_MGL on 2006-11-06 23:25:17 as
	Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 836-844. by Stewart B. Kirton, Christopher W. Murray, Marcel L. Verdonk, Richard D. Taylor posted to p450 by yongzhao to the group TSRI_MGL on 2006-11-02 01:38:26 as
	Recent Advances in Docking and Scoring [My Copy] Current Computer - Aided Drug Design, Vol. 1, No. 1. (January 2005), pp. 93-102. by E. M. Krovat, T. Steindl, T. Langer posted to docking docking_design review score by yongzhao to the group TSRI_MGL on 2006-10-30 22:38:36 as along with 2 people kazemi pmalatino
	Docking and scoring in virtual screening for drug discovery: methods and applications. [My Copy] Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949. by D. B. Kitchen, H. Decornez, J. R. Furr, J. Bajorath posted to screening by yongzhao to the group TSRI_MGL on 2006-10-30 22:37:00 as along with 8 people and 8 groups LamBras robert85 BragilMassoud dgruiz beapen anita marcius sangeetha Bioinformatics structure-bii Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
	M-score: a knowledge-based potential scoring function accounting for protein atom mobility. [My Copy] J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5903-5911. by C. Y. Yang, R. Wang, S. Wang posted to docking_design score by yongzhao to the group TSRI_MGL on 2006-10-26 18:33:56 as along with 2 people mijam kazemi
	Benchmarking Sets for Molecular Docking [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6789-6801. by Niu Huang, Brian K. Shoichet, John J. Irwin posted to docking docking_design library potential_app by yongzhao to the group TSRI_MGL on 2006-10-26 18:11:12 as along with 4 people GermanErlenkamp ihaque BragilMassoud daevans
	A review of protein-small molecule docking methods [My Copy] Journal of Computer-Aided Molecular Design, Vol. V16, No. 3. (1 March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted to docking_design review by yongzhao to the group TSRI_MGL on 2006-10-25 00:18:37 as
	Dynamite: a simple way to gain insight into protein motions. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 60, No. Pt 12 Pt 1. (01 December 2004), pp. 2280-2287. by C. Paul Barrett, Benjamin A. Hall, Martin E. Noble posted to conformation_sampling flex by yongzhao to the group TSRI_MGL on 2006-10-24 02:58:49 as along with 4 people arifor dimka aqeel choonpeng
	Comparing protein-ligand docking programs is difficult. [My Copy] Proteins (3 June 2005) by Jason C C. Cole, Christopher W W. Murray, J Willem M W. Nissink, Richard D D. Taylor, Robin Taylor posted to docking_design review by yongzhao to the group TSRI_MGL on 2006-10-18 20:51:13 as along with 8 people and 2 groups flbarroso BragilMassoud dgruiz thaliana sangeetha kzfm peprovy carlescorbi Bioinformatics insilicodrug
	Molecular Symmetry Perception [My Copy] J. Chem. Inf. Model., Vol. 44, No. 2. (22 March 2004), pp. 596-600. by J. Ivanov posted to no-tag by yongzhao to the group TSRI_MGL on 2006-10-14 01:00:19 as
	EMAN: semiautomated software for high-resolution single-particle reconstructions. [My Copy] Journal of structural biology, Vol. 128, No. 1. (1 December 1999), pp. 82-97. by S. J. Ludtke, P. R. Baldwin, W. Chiu posted to cryoem by yongzhao to the group TSRI_MGL on 2006-10-04 00:22:39 as along with 4 people and 2 groups wxvrqs dawnsong jwm faion Radiation_Damage Stressosome
	Current status of virtual screening as analysed by target class. [My Copy] Med Chem, Vol. 2, No. 1. (January 2006), pp. 89-112. by M. J. Stoermer posted to screening by yongzhao to the group TSRI_MGL on 2006-09-20 18:55:14 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 6. (c 2004), pp. 2114-2125. by R. Wang, Y. Lu, X. Fang, S. Wang posted to score by yongzhao to the group TSRI_MGL on 2006-09-20 18:04:05 as along with 1 person BragilMassoud
	New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy [My Copy] Journal of Computational Chemistry, Vol. 26, No. 11. (2005), pp. 1089-1095. by A. M. Ruvinsky, A. V. Kozintsev posted to docking reranking by yongzhao to the group TSRI_MGL on 2006-09-14 22:21:58 as along with 1 person daevans
	Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. [My Copy] J Med Chem, Vol. 48, No. 16. (11 August 2005), pp. 5108-5111. by D. Huang, U. Lüthi, P. Kolb, et al.K. Edler, M. Cecchini, S. Audetat, A. Barberis, A. Caflisch posted to bace screening by yongzhao to the group TSRI_MGL on 2006-09-14 02:50:52 as along with 1 person and 3 groups joergkurtwegner Molecular-Modelling Drug-Design Cheminformatics
	Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. [My Copy] Protein science : a publication of the Protein Society, Vol. 11, No. 2. (1 February 2002), pp. 184-197. by Buyong Ma, Maxim Shatsky, Haim J. Wolfson, Ruth Nussinov posted to docking_design induced_fit multiple by yongzhao to the group TSRI_MGL on 2006-09-13 22:41:06 as along with 3 people ubcg08l ruvido jlh64
	Further development and validation of empirical scoring functions for structure-based binding affinity prediction. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 1. (January 2002), pp. 11-26. by R. Wang, L. Lai, S. Wang posted to docking docking_design by yongzhao to the group TSRI_MGL on 2006-09-13 20:11:22 as along with 1 person BragilMassoud
	DrugScore(CSD)-Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction. [My Copy] J Med Chem, Vol. 48, No. 20. (6 October 2005), pp. 6296-6303. by Hans F. Velec, Holger Gohlke, Gerhard Klebe posted to docking_design by yongzhao to the group TSRI_MGL on 2006-09-08 05:18:38 as along with 4 people BragilMassoud apostola insilico ucbcjbm
	Improving binding mode predictions by docking into protein-specifically adapted potential fields. [My Copy] J Med Chem, Vol. 48, No. 17. (25 August 2005), pp. 5466-5479. by S. Radestock, M. Böhm, H. Gohlke posted to docking potential_app by yongzhao to the group TSRI_MGL on 2006-09-08 01:51:42 as along with 3 people BragilMassoud kazemi naitsabes
	Receptor-Ligand Binding Sites and Virtual Screening [My Copy] pp. 1283-1304. by Hattotuwagama,, Channa, K. posted to screening by yongzhao to the group TSRI_MGL on 2006-09-08 00:00:06 as
	Modeling of Cdc25B Dual Specifity Protein Phosphatase Inhibitors: Docking of Ligands and Enzymatic Inhibition Mechanism [My Copy] ChemMedChem, Vol. 1, No. 5. (2006), pp. 540-550. by Antonio Lavecchia, Sandro Cosconati, Vittorio Limongelli, Ettore Novellino posted to no-tag by yongzhao to the group TSRI_MGL on 2006-08-30 00:11:57 as along with 1 person apaydin

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docking	146
lox-1	75
dna	46
coiled_coil	40
docking_prog	38
cepa	32
programmi	24
drug_design	20
dna_nanostructures	19
neck_domain	16
topo	15
cluster_analysis	12
figata	11
adducts	8
algorithm	8
molecular_dynamics	7
implicit_solvent	6
znua	5
methods	4
protein-peptide_dock	4
structure_prediction	4
circular_dichroism	3
cpt	3
domain_movement	3
ambertools	2
artificial_intelligence	2
chiancone	2
coarse_grained	2
guidelines	2
inibitori	2
modelling	2
mordor	2
namd	2
nmr_and_md	2
peptide	2
protein-protein_dock	2
ricerche	2
user_manual	2
analysis_prog	1
carrier	1
database	1
electrostatic	1
electrostatics	1
fleksy	1
initial_screening	1
langevin	1
lipid	1
nanocage	1
papvir	1
pedc	1
protein-protein_docking	1
qsar	1
rna	1
server	1

oteri's watchlist [151 articles] Export

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