BragilMassoud's energyfunctions [42 articles] Export

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	Accelerating molecular modeling applications with graphics processors [My Copy] Journal of Computational Chemistry, Vol. 28, No. 16. (25 September 2007), pp. 2618-2640. by John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten posted to energyfunctions forcefield gpu by BragilMassoud on 2007-09-28 16:56:49 as along with 9 people and 1 group ihaque naoya charris5 timg ruvido sobolevnrm yalexeev mikaellund afenley baker-group
	Potential energy functions for protein design. [My Copy] Curr Opin Struct Biol (24 March 2007) by F Edward E. Boas, Pehr B B. Harbury posted to design energyfunctions protein review structure by BragilMassoud on 2007-05-08 13:32:47 as along with 5 people kgutwin krapnik msuarezdiez aalibes onufriev
	Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions. [My Copy] J Comput Chem (2 April 2007) by Stephan Raub, Christel M M. Marian posted to electrostatics energyfunctions qc by BragilMassoud on 2007-04-07 12:37:03 as
	A new implicit solvent model for protein-ligand docking. [My Copy] Proteins (28 February 2007) by Antonio Morreale, Rubén Gil-Redondo, Angel R R. Ortiz posted to docking electrostatics energyfunctions by BragilMassoud on 2007-03-04 13:30:32 as along with 1 person flbarroso
	Gaussian docking functions [My Copy] Biopolymers, Vol. 68, No. 1. (2003), pp. 76-90. by Mark R. Mcgann, Harold R. Almond, Anthony Nicholls, Andrew J. Grant, Frank K. Brown posted to docking energyfunctions openeye by BragilMassoud on 2007-02-19 11:10:26 as along with 1 person ima
	Supervised Consensus Scoring for Docking and Virtual Screening. [My Copy] J Chem Inf Model (13 February 2007) by Reiji Teramoto, Hiroaki Fukunishi posted to docking energyfunctions screening by BragilMassoud on 2007-02-15 16:59:15 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 solvation screening forcefield energyfunctions docking autodock by BragilMassoud on 2007-02-04 15:03:24 as along with 6 people and 1 group trishul nickolay joule oteri IrinaMoreira carlescorbi Structural Biology Group TorVergata
	Strong and weak hydrogen bonds in the protein-ligand interface. [My Copy] Proteins (5 January 2007) by Sunil K K. Panigrahi, Gautam R R. Desiraju posted to docking energyfunctions hond by BragilMassoud on 2007-01-10 14:30:44 as along with 3 people and 1 group Lombardo_7 cat_worth friendpine structural_bioinformatics
	Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization? [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 25. (1 December 2006), pp. 7427-7439. by Julien Michel, Marcel L. Verdonk, Jonathan W. Essex posted to affinity docking energyfunctions screening solvation by BragilMassoud on 2006-12-09 15:39:15 as along with 1 person daevans
	Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. [My Copy] Proteins (26 October 2006) by Sumeet Salaniwal, Eric S. S. Manas, Juan C. C. Alvarez, Rayomand J. J. Unwalla posted to affinity energyfunctions entropy screening by BragilMassoud on 2006-10-29 16:42:53 as along with 1 person cat_worth
	PMF Scoring Revisited [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 20. (1 October 2006), pp. 5895-5902. by Ingo Muegge posted to affinitiy docking electrostatics energyfunctions screening by BragilMassoud on 2006-09-30 14:24:46 as along with 3 people nickolay ucbcjbm peprovy
	A Critical Assessment of Docking Programs and Scoring Functions [My Copy] J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5912-5931. by G. L. Warren, C. W. Andrews, A. M. Capelli, et al.B. Clarke, J. Lalonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head posted to docking energyfunctions review by BragilMassoud on 2006-09-30 14:24:23 as along with 6 people skoddet ucbcjbm aalibes schlauchi daevans superpyrin
	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] J Comput Aided Mol Des, Vol. 12, No. 4. (July 1998), pp. 309-323. by H. J. Boehm posted to design docking energyfunctions ludi by BragilMassoud on 2006-08-01 22:56:15 as
	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] J Comput Aided Mol Des, Vol. 8, No. 3. (June 1994), pp. 243-256. by H. J. Boehm posted to design docking energyfunctions ludi by BragilMassoud on 2006-08-01 22:55:48 as along with 4 people nachtalp nickolay papatonyhill schlauchi
	Ligand bias of scoring functions in structure-based virtual screening. [My Copy] J Chem Inf Model, Vol. 46, No. 3. (n 2006), pp. 1334-1343. by M. Jacobsson, A. Karlén posted to affinity energyfunctions screening by BragilMassoud on 2006-07-28 18:00:02 as
	Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. [My Copy] Proteins, Vol. 60, No. 4. (1 September 2005), pp. 629-643. by S. Cotesta, F. Giordanetto, J. Y. Trosset, et al.P. Crivori, R. T. Kroemer, P. F. Stouten, A. Vulpetti posted to affinity docking energyfunctions kinases screening by BragilMassoud on 2006-07-11 20:30:21 as
	Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein-Ligand Complexes [My Copy] J. Chem. Inf. Model., Vol. 46, No. 1. (23 January 2006), pp. 380-391. by A. Oda, K. Tsuchida, T. Takakura, N. Yamaotsu, S. Hirono posted to docking energyfunctions by BragilMassoud on 2006-06-30 20:56:38 as along with 1 person ucbcjbm
	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 affinity docking energyfunctions screening by BragilMassoud on 2006-06-29 14:11:29 as along with 1 person and 1 group yongzhao TSRI_MGL
	Validation and use of the MM-PBSA approach for drug discovery. [My Copy] J Med Chem, Vol. 48, No. 12. (16 June 2005), pp. 4040-4048. by B. Kuhn, P. Gerber, T. Schulz-Gasch, M. Stahl posted to affinity docking electrostatics energyfunctions screening by BragilMassoud on 2006-06-24 11:28:43 as along with 4 people and 1 group apostola mleis gcaltabiano LamBras LabCompMed
	Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. [My Copy] J Comput Aided Mol Des, Vol. 10, No. 5. (October 1996), pp. 427-440. by A. N. Jain posted to docking energyfunctions screening surflex by BragilMassoud on 2006-06-20 16:38:54 as
	Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids [My Copy] Journal of the American Chemical Society, Vol. 118, No. 45. (1 January 1996), pp. 11225-11236. by William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives posted to docking energyfunctions forcefield by BragilMassoud on 2006-05-23 12:54:51 as along with 9 people dimka snichols15 flbarroso tovrstra dfgreen sunnytov loison softsimu Diego_Prada
	An improved hydrogen bond potential: impact on medium resolution protein structures. [My Copy] Protein Sci, Vol. 11, No. 6. (June 2002), pp. 1415-1423. by F. Fabiola, R. Bertram, A. Korostelev, M. S. Chapman posted to docking energyfunctions forcefield hbond md by BragilMassoud on 2006-04-20 15:09:39 as along with 2 people chiufanlee anonymousarun
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted to affinity electrostatics energyfunctions md review by BragilMassoud on 2006-03-19 16:29:37 as along with 7 people oteri r2s2 flbarroso LamBras qwermish RamuAnandakrishnan jteyra
	Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data [My Copy] Journal of medicinal chemistry (2005) by T. A. Pham, A. N. Jain posted to docking energyfunctions screening surflex by BragilMassoud on 2006-02-11 15:42:52 as
	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 docking energyfunctions review screening by BragilMassoud on 2006-02-04 15:51:20 as along with 8 people and 9 groups LamBras robert85 dgruiz beapen anita yongzhao marcius sangeetha Bioinformatics structure-bii TSRI_MGL Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
	SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex [My Copy] Journal of Molecular Modeling, Vol. 4, No. 12. (December 1998), pp. 379-394. by Wang Renxiao, Liu Liang, Lai Luhua, Tang Youqi posted to affinity docking energyfunctions screening by BragilMassoud on 2006-01-09 13:46:03 as
	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 affinity docking energyfunctions screening by BragilMassoud on 2006-01-09 13:14:18 as along with 1 person and 1 group yongzhao TSRI_MGL
	PSI-DOCK: Towards highly efficient and accurate flexible ligand docking. [My Copy] Proteins (4 January 2006) by Jianfeng Pei, Qi Wang, Zhenming Liu, Qingliang Li, Kun Yang, Luhua Lai posted to docking energyfunctions by BragilMassoud on 2006-01-08 17:10:06 as
	What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. [My Copy] J Comput Chem, Vol. 27, No. 1. (January 2006), pp. 72-89. by Z. Yu, M. P. Jacobson, R. A. Friesner posted to electrostatics energyfunctions protein by BragilMassoud on 2005-12-29 09:44:51 as along with 3 people and 1 group qzhang choonpeng onufriev TSRI_MGL
	Empirical force fields for biological macromolecules: overview and issues. [My Copy] Journal of computational chemistry, Vol. 25, No. 13. (1 October 2004), pp. 1584-1604. by A. D. Mackerell posted to energyfunctions forcefield md by BragilMassoud on 2005-11-29 18:34:05 as along with 7 people and 3 groups flbarroso whitead marcius dgront loison mirzazadeh AndreaColetta Jiang Research Group BioinfoCIPF SGU-CIPF
	New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities [My Copy] Journal of Computational Chemistry, Vol. 17, No. 9. (7 December 1998), pp. 1132-1141. by Arnaud Blondel, Martin Karplus posted to energyfunctions forcefield md by BragilMassoud on 2005-11-29 13:04:14 as along with 1 person nachtalp
	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 affinity docking energyfunctions screening by BragilMassoud on 2005-10-02 17:29:54 as along with 4 people and 1 group apostola yongzhao insilico ucbcjbm TSRI_MGL
	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 energyfunctions by BragilMassoud on 2005-09-07 10:11:46 as along with 3 people and 1 group yongzhao kazemi naitsabes TSRI_MGL
	Binding MOAD (Mother Of All Databases). [My Copy] Proteins (21 June 2005) by Liegi Hu, Mark L L. Benson, Richard D D. Smith, Michael G G. Lerner, Heather A A. Carlson posted to affinity db docking energyfunctions ligands protein structure by BragilMassoud on 2005-06-24 14:16:20 as along with 5 people and 10 groups sangeetha shantanu caporaso papatonyhill higueruelo structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology biomedical-nlp insilicodrug
	Modified AutoDock for accurate docking of protein kinase inhibitors. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 2. (February 2002), pp. 113-127. by O. V. Buzko, A. C. Bishop, K. M. Shokat posted to docking energyfunctions kinases protein screening by BragilMassoud on 2005-06-16 13:51:59 as
	Evaluation of library ranking efficacy in virtual screening. [My Copy] J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 11-22. by M. Kontoyianni, G. S. Sokol, L. M. McClellan posted to docking energyfunctions screening by BragilMassoud on 2005-05-10 16:15:47 as along with 3 people and 2 groups nachtalp marcius schuwi BioinfoCIPF SGU-CIPF
	Flexible docking using Tabu search and an empirical estimate of binding affinity. [My Copy] Proteins, Vol. 33, No. 3. (15 November 1998), pp. 367-382. by C. A. Baxter, C. W. Murray, D. E. Clark, D. R. Westhead, M. D. Eldridge posted to docking energyfunctions by BragilMassoud on 2005-05-08 17:49:49 as along with 1 person blackbart
	Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. [My Copy] J Comput Aided Mol Des, Vol. 12, No. 5. (September 1998), pp. 503-519. by C. W. Murray, T. R. Auton, M. D. Eldridge posted to docking energyfunctions screening by BragilMassoud on 2005-05-08 17:49:09 as
	Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. [My Copy] J Comput Aided Mol Des, Vol. 11, No. 5. (September 1997), pp. 425-445. by M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini, R. P. Mee posted to docking energyfunctions screening by BragilMassoud on 2005-05-08 17:48:38 as along with 2 people nachtalp schlauchi
	Improved protein-ligand docking using GOLD. [My Copy] Proteins, Vol. 52, No. 4. (1 September 2003), pp. 609-623. by M. L. Verdonk, J. C. Cole, M. J. Hartshorn, C. W. Murray, R. D. Taylor posted to docking energyfunctions gold by BragilMassoud on 2005-05-08 17:47:26 as
	Assessing scoring functions for protein-ligand interactions. [My Copy] J Med Chem, Vol. 47, No. 12. (3 June 2004), pp. 3032-3047. by P. Ferrara, H. Gohlke, D. J. Price, G. Klebe, C. L. Brooks posted to affinity docking energyfunctions screening by BragilMassoud on 2005-05-08 17:40:35 as along with 3 people oteri AliceWang nachtalp
	Native atom types for knowledge-based potentials: application to binding energy prediction. [My Copy] J Med Chem, Vol. 47, No. 18. (26 August 2004), pp. 4538-4558. by B. N. Dominy, E. I. Shakhnovich posted to docking energyfunctions by BragilMassoud on 2005-05-08 17:29:21 as

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docking	175
structure	91
protein	89
screening	84
pharmacology	43
energyfunctions	42
review	38
math	35
nma	25
affinity	22
forcefield	21
kinases	21
ligands	20
flexible_protein	18
minimization	18
robert	17
db	13
hts	13
md	13
visualization	13
internal_coordinates	12
alignment	11
superposition	11
actin	10
electrostatics	9
gold	9
evolution	8
kinesin	7
ligand	7
dehydron	6
design	6
solvation	6
cavities	5
flexx	5
machinelearning	5
mc	5
specificity	5
statistics	5
stun	5
surflex	5
conformations	4
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glide	4
metabolomics	4
pts	4
qc	4
slide	4
antibiotics	3
autodock	3
benchmark	3
benchmarks	3
brain	3
comment	3
comparison	3
est	3
fingerprints	3
graphs	3
inversescreening	3
physics	3
ribbons	3
roc	3
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abinitio	2
born	2
cancer	2
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consensus	2
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energy_functions	2
enzyme	2
enzymes	2
ga	2
geneexpression	2
graph	2
ludi	2
pharmacogenetics	2
pharmacophore	2
quaternion	2
ring_flipping	2
similarity	2
tox	2
1acj	1
adme	1
affinitiy	1
algorithm	1
antidepressants	1
antoptimization	1
bench_errors	1
bias	1
clustering	1
conforamtions	1
conformaations	1
conformation	1
denovo	1
density	1
dock	1
dokcing	1
ehits	1
entropy	1
fragmentation	1
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geometry	1
ghb	1
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gpu	1
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hbond	1
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inverse_screening	1
kinase	1
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BragilMassoud's energyfunctions [42 articles] Export

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