nickolay's library 242 articles Export

	Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sourav Das, Arshad Kokardekar, Curt M. Breneman posted to surface shape rapid comparison binding_site algorithm by nickolay on 2009-11-18 16:39:24 as
	Structure-Based Predictive Models for Allosteric Hot Spots [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000531. by Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell posted to structure prediction model hot_spots allostery by nickolay on 2009-11-04 16:08:16 as along with 3 people and 1 group apaydin klexa barry McCammon
	Do Biologically Relevant Compounds Have More Chance To Be Drugs? [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 10. (26 October 2009), pp. 2376-2381. by De-Xin Kong, Wei Ren, Wei Lü, Hong-Yu Zhang posted to nov09 drug_discovery_and_development biological_relevance by nickolay on 2009-11-03 21:22:54 as
	Mapping Human Metabolic Pathways in the Small Molecule Chemical Space [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 10. (26 October 2009), pp. 2272-2289. by Antonio Macchiarulo, Janet M. Thornton, Irene Nobeli posted to small pathway nov09 metabolome mapping drug classification by nickolay on 2009-11-03 21:17:48 as
	MISTRAL: a tool for energy-based multiple structural alignment of proteins [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2663-2669. by Cristian Micheletti, Henri Orland posted to software nov09 multiple_structural_alignment energy_minimization alignment algorithm by nickolay on 2009-11-03 21:08:02 as along with 2 people and 1 group jforment reyez Bioinformatics Core Service
	A novel and efficient tool for locating and characterizing protein cavities and binding sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (11 September 2009), NA. by Ashutosh Tripathi, Glen E. Kellogg posted to nov09 identification binding_site by nickolay on 2009-11-03 20:50:02 as along with 2 people higueruelo ahmetbakan
	Structure of Protein Interaction Networks and Their Implications on Drug Design [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (30 October 2009), e1000550. by Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano posted to protein-protein nov09 network drug by nickolay on 2009-11-03 20:45:42 as along with 9 people and 1 group kiekyon kshameer zwang phoenixzxl venancio CorinYeats ess30 poirel jbesnard Orengo Group Journal Picks
	Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (30 October 0000), 091030094710018. by Zsolt Lepp, Chunfei Huang, Takashi Okada posted to similarity nov09 network molecule ligand compound_libraries cheminformatics by nickolay on 2009-11-03 20:39:55 as along with 1 person massivemayhem
	Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Pablo Englebienne, Nicolas Moitessier posted to solvent prediction nov09 ligand flexibility docking affinity by nickolay on 2009-11-03 20:35:14 as
	3D-SURFER: software for high-throughput protein surface comparison and analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2843-2844. by David La, Juan Esquivel-Rodriguez, Vishwesh Venkatraman, et al.Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara posted to surface software protein nov09 comparison by nickolay on 2009-10-23 17:57:57 as along with 3 people and 1 group operon kshameer renatomilani structural_bioinformatics
	Algorithms for optimal protein structure alignment [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2751-2756. by Aleksandar Poleksic posted to structure protein nov09 alignment algorithm by nickolay on 2009-10-23 17:56:15 as along with 5 people and 1 group barry operon kshameer kevinzheng1983 neils structural_bioinformatics
	A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (21 August 2009), e1000474. by James C. Adams, Michael J. Keiser, Li Basuino, et al.Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt posted to nov09 target similarity network metabolism ligand drug action by nickolay on 2009-10-08 19:20:47 as along with 8 people and 1 group sobolevnrm klexa bdessailly pablocarb ptrobajo biomcgary reyez thomaskelder Orengo Group Journal Picks
	Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000470. by Mati Cohen, Vladimir Potapov, Gideon Schreiber posted to nov09 residue metric knowledge-based-potentials interaction distance by nickolay on 2009-10-08 19:16:47 as along with 6 people klexa Diego_Prada zwang reyez TRHvidsten ericrpaquet
	Quantifying the Relationships among Drug Classes [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 4. (1 April 2008), pp. 755-765. by Jérôme Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet posted to nov09 similarity-network ligand drug clustering by nickolay on 2009-10-08 19:11:43 as along with 8 people and 1 group tjchen mijogiffin pauldobson dullhunk middledomain sobolevnrm ucbcjbm jerome_ucsf_slb baker-group
	Accuracy analysis of multiple structure alignments [My Copy] Protein Science, Vol. 18, No. 10. (October 2009), pp. 2027-2035. by Christoph Berbalk, Christine S. Schwaiger, Peter Lackner posted to nov09 by nickolay on 2009-10-07 15:21:24 as along with 1 person klexa
	Identification of protein functional surfaces by the concept of a split pocket [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 959-976. by Yan Y. Tseng, Wen-Hsiung Li posted to site protein oct09 identification binding by nickolay on 2009-10-07 15:11:46 as along with 1 person and 1 group AliC Orengo Group Journal Picks
	QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1974-1985. by Robert P. Sheridan, Kiyean Nam, Vladimir N. Maiorov, Daniel R. McMasters, Wendy D. Cornell posted to qsar oct09 kinase binding by nickolay on 2009-10-07 01:38:50 as
	An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1866-1870. by Pierre Baldi, Daniel S. Hirschberg posted to tanimoto similarity oct09 ligand cheminformatics by nickolay on 2009-10-07 01:36:53 as
	Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 61, No. Pt 9. (September 2005), pp. 1199-1206. by Jodie M. Johnston, Vickery L. Arcus, Edward N. Baker posted to p2 by nickolay on 2009-09-10 19:42:18 as
	Crystal structure of the C47S mutant of human peroxiredoxin 5 [My Copy] Journal of Chemical Crystallography, Vol. 34, No. 8. (1 August 2004), pp. 553-558. by Christine Evrard, Aude Smeets, Bernard Knoops, Jean-Paul Declercq posted to p2 by nickolay on 2009-09-10 19:40:44 as
	Crystal Structure of the PTEN Tumor SuppressorImplications for Its Phosphoinositide Phosphatase Activity and Membrane Association [My Copy] Cell, Vol. 99, No. 3. (29 October 1999), pp. 323-334. by Jie-Oh Lee, Haijuan Yang, Maria-Magdalena Georgescu, et al.Antonio Di Cristofano, Tomohiko Maehama, Yigong Shi, Jack E. Dixon, Pier Pandolfi, Nikola P. Pavletich posted to p2 by nickolay on 2009-09-10 19:38:56 as
	Biophysical Studies of eIF4E Cap-binding Protein: Recognition of mRNA 5′ Cap Structure and Synthetic Fragments of eIF4G and 4E-BP1 Proteins [My Copy] Journal of Molecular Biology, Vol. 319, No. 3. (07 June 2002), pp. 615-635. by Anna Niedzwiecka, Joseph Marcotrigiano, Janusz Stepinski, et al.Marzena Jankowska-Anyszka, Aleksandra Wyslouch-Cieszynska, Michal Dadlez, Anne-Claude Gingras, Pawel Mak, Edward Darzynkiewicz, Nahum Sonenberg posted to p2 by nickolay on 2009-09-10 19:36:25 as
	Imidazo61,2-a9pyridines: A potent and selective class of cyclin-Dependent kinase inhibitors identified through structure-Based hybridisation [My Copy] Bioorganic & Medicinal Chemistry Letters, Vol. 13, No. 18. (September 2003), pp. 3021-3026. by M. Anderson posted to p2 by nickolay on 2009-09-10 19:35:05 as
	Free energy requirement for domain movement of an enzyme. [My Copy] The Journal of biological chemistry, Vol. 275, No. 25. (23 June 2000), pp. 18939-18945. by J. Ishijima, T. Nakai, S. Kawaguchi, K. Hirotsu, S. Kuramitsu posted to p2 by nickolay on 2009-09-10 19:33:55 as along with 1 person pablocarb
	Structure of Human Epoxide Hydrolase Reveals Mechanistic Inferences on Bifunctional Catalysis in Epoxide and Phosphate Ester Hydrolysis†,‡ [My Copy] Biochemistry, Vol. 43, No. 16. (1 April 2004), pp. 4716-4723. by German A. Gomez, Christophe Morisseau, Bruce D. Hammock, David W. Christianson posted to p2 by nickolay on 2009-09-10 19:31:34 as
	Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding [My Copy] Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 21-28. by A. Gutteridge, J. Thornton posted to p2 by nickolay on 2009-09-10 15:56:06 as along with 8 people and 1 group boris_aguilar carlosjavierna baaden lna yongzhao alexg gbart noby TSRI_MGL
	Structural biology of zinc. [My Copy] Advances in protein chemistry, Vol. 42 (1991), pp. 281-355. by D. W. Christianson posted to p2 by nickolay on 2009-09-10 15:42:54 as
	UCSF Chimera--a visualization system for exploratory research and analysis. [My Copy] Journal of computational chemistry, Vol. 25, No. 13. (October 2004), pp. 1605-1612. by Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, et al.Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin posted to p2 by nickolay on 2009-09-10 15:39:59 as along with 8 people and 3 groups whitead robert A_Coletta_Thesis happy_manatee sobolevnrm saunders sjanusz dna Jiang Research Group Structural Biology Group TorVergata baker-group
	Efficient molecular docking of NMR structures: application to HIV-1 protease. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 1. (1 January 2007), pp. 43-51. by Sheng-You Y. Huang, Xiaoqin Zou posted to p2 by nickolay on 2009-09-10 15:32:58 as along with 2 people dgruiz hmk
	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 p2 docking by nickolay on 2009-09-10 15:31:39 as along with 8 people and 2 groups oteri AliceWang BragilMassoud bicko yongzhao kazemi hmk LamBras Structural Biology Group TorVergata TSRI_MGL
	An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function [My Copy] Journal of Computational Chemistry, Vol. 27, No. 15. (2006), pp. 1876-1882. by Sheng-You Huang, Xiaoqin Zou posted to p2 by nickolay on 2009-09-10 15:30:10 as
	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 p2 force-field by nickolay on 2009-09-10 15:29:08 as along with 5 people and 1 group joule oteri IrinaMoreira BragilMassoud carlescorbi Structural Biology Group TorVergata
	Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function [My Copy] Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1998), pp. 1639-1662. by Garrett M. Morris, David S. Goodsell, Robert S. Halliday, et al.Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson posted to p2 docking by nickolay on 2009-09-10 15:23:13 as along with 22 people and 2 groups npt11tpn jamalex joule lna Lombardo_7 karinaecomp oteri A_Coletta_Thesis arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain LamBras andreramme UVA_mag_res Chang group TSRI_MGL
	DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases [My Copy] Journal of Computer-Aided Molecular Design, Vol. 15, No. 5. (1 May 2001), pp. 411-428. by Todd J. A. Ewing, Shingo Makino, A. Geoffrey Skillman, Irwin D. Kuntz posted to p2 docking by nickolay on 2009-09-10 15:21:44 as along with 1 person willpitt
	Further development and validation of empirical scoring functions for structure-based binding affinity prediction [My Copy] Journal of Computer-Aided Molecular Design, Vol. 16, No. 1. (1 January 2002), pp. 11-26. by Renxiao Wang, Luhua Lai, Shaomeng Wang posted to scoring-functions prediction p2 affinity by nickolay on 2009-09-10 15:20:38 as along with 1 person GermanErlenkamp
	Comparative Evaluation of 11 Scoring Functions for Molecular Docking [My Copy] Journal of Medicinal Chemistry, Vol. 46, No. 12. (1 June 2003), pp. 2287-2303. by Renxiao Wang, Yipin Lu, Shaomeng Wang posted to p2 by nickolay on 2009-09-10 01:53:15 as along with 4 people dgruiz P2324548 peprovy schlauchi
	The Protein Data Bank [My Copy] Acta Crystallographica Section D, Vol. 58, No. 6 Part 1. (Jun 2002), pp. 899-907. by Helen M. Berman, Tammy Battistuz, T. N. Bhat, et al.Wolfgang F. Bluhm, Philip E. Bourne, Kyle Burkhardt, Zukang Feng, Gary L. Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, Veerasamy Ravichandran, Bohdan Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook, Christine Zardecki posted to p2 by nickolay on 2009-09-10 01:52:14 as
	An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials [My Copy] Journal of Computational Chemistry, Vol. 27, No. 15. (2006), pp. 1866-1875. by Sheng-You Huang, Xiaoqin Zou posted to p2 by nickolay on 2009-09-10 01:51:02 as along with 2 people mijam Evangelia
	PMF Scoring Revisited [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 20. (1 October 2006), pp. 5895-5902. by Ingo Muegge posted to p2 by nickolay on 2009-09-10 01:48:23 as along with 3 people ucbcjbm BragilMassoud peprovy
	A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes [My Copy] Journal of Medicinal Chemistry, Vol. 48, No. 7. (1 April 2005), pp. 2325-2335. by Chi Zhang, Song Liu, Qianqian Zhu, Yaoqi Zhou posted to p2 by nickolay on 2009-09-10 01:47:10 as along with 1 person P2324548
	Knowledge-based analysis of microarray gene expression data by using support vector machines. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 1. (4 January 2000), pp. 262-267. by M. P. Brown, W. N. Grundy, D. Lin, et al.N. Cristianini, C. W. Sugnet, T. S. Furey, M. Ares, D. Haussler posted to p2 by nickolay on 2009-09-10 01:46:22 as along with 7 people and 4 groups barmak7282 seb1 akshayk petrposik neveaire dps srp33 Biostatistics Computational-Genomics Bioinformatics Neuroscience
	BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential [My Copy] Journal of Computational Chemistry, Vol. 20, No. 11. (1999), pp. 1165-1176. by John B. O. Mitchell, Roman A. Laskowski, Alexander Alex, Janet M. Thornton posted to p2 by nickolay on 2009-09-10 01:45:24 as along with 1 person ucbcjbm
	A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach [My Copy] Journal of Medicinal Chemistry, Vol. 42, No. 5. (1 March 1999), pp. 791-804. by Ingo Muegge, Yvonne C. Martin posted to p2 by nickolay on 2009-09-10 01:44:04 as along with 1 person schlauchi
	SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence [My Copy] Journal of the American Chemical Society, Vol. 118, No. 47. (1 January 1996), pp. 11733-11744. by Robert S. DeWitte, Eugene I. Shakhnovich posted to p2 by nickolay on 2009-09-10 01:43:28 as along with 1 person apostola
	Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity [My Copy] Protein Engineering, Design and Selection, Vol. 8, No. 7. (1 July 1995), pp. 677-691. by G. Verkhivker, K. Appelt, S. T. Freer, J. E. Villafranca posted to p2 by nickolay on 2009-09-10 01:38:19 as
	Empirical potentials and functions for protein folding and binding [My Copy] Current Opinion in Structural Biology, Vol. 7, No. 2. (April 1997), pp. 222-228. by S. Vajda posted to p2 by nickolay on 2009-09-10 01:36:44 as
	An attempt to analyse progress in fold recognition from CASP1 to CASP3 [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 226-230. by Manfred J. Sippl, Peter Lackner, Francisco S. Domingues, Walter A. Koppensteiner posted to p2 by nickolay on 2009-09-10 01:35:56 as
	Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs [My Copy] Journal of Computer-Aided Molecular Design, Vol. 12, No. 4. (1 July 1998), pp. 309-309. by Hans-Joachim Böhm posted to p2 by nickolay on 2009-09-10 01:31:58 as along with 1 person boris_aguilar
	Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes [My Copy] Journal of Computer-Aided Molecular Design, Vol. 11, No. 5. (1 September 1997), pp. 425-445. by Matthew D. Eldridge, Christopher W. Murray, Timothy R. Auton, Gaia V. Paolini, Roger P. Mee posted to p2 by nickolay on 2009-09-10 01:31:08 as along with 1 person boris_aguilar
	The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure [My Copy] Journal of Computer-Aided Molecular Design, Vol. 8, No. 3. (1 June 1994), pp. 243-256. by Hans-Joachim Böhm posted to p2 by nickolay on 2009-09-10 01:30:41 as

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p2	56
binding	47
protein	42
algorithm	35
protein-ligand	32
to-be-tagged	31
structure	29
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prediction	25
bibtex-import	22
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msa	5
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structure-searching	5
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amino-acids	4
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function	4
geometric	4
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interaction	4
network	4
protein-interface	4
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software	4
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affinity	3
cadd	3
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printed	3
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binding_site	2
chemistry	2
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clique	2
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server	1
shape	1
simulation	1
tanimoto	1
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topology	1
visualization	1
web-based	1

nickolay's library 242 articles Export

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