BragilMassoud's protein [89 articles] Export

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	Progress in computational protein design [My Copy] Current Opinion in Biotechnology, Vol. 18, No. 4. (17 August 2007), pp. 305-311. by S. Lippow, B. Tidor posted to design protein review structure by BragilMassoud on 2007-09-17 17:58:44 as along with 3 people and 1 group baiaixi Lombardo_7 msuarezdiez Bioinformatics
	Visualization software for molecular assemblies [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Thomas D. Goddard, Thomas E. Ferrin posted to protein structure visualization by BragilMassoud on 2007-09-10 13:36:11 as along with 4 people and 1 group guhjy sobolevnrm higueruelo dgront baker-group
	Improved sampling methods for molecular simulation. [My Copy] Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 187-191. by H. Lei, Y. Duan posted to math minimization protein review structure by BragilMassoud on 2007-05-08 13:33:48 as along with 3 people viktor21614 aqeel allmensch
	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
	A simple way to compute protein dynamics without a mechanical model. [My Copy] Proteins (13 April 2007) by Chien-Hua H. Shih, Shao-Wei W. Huang, Shih-Chung C. Yen, Yan-Long L. Lai, Sung-Huan H. Yu, Jenn-Kang K. Hwang posted to nma protein structure by BragilMassoud on 2007-04-20 14:19:53 as along with 3 people bicko cactus jlh64
	Joint neighbors approximation of macromolecular solvent accessible surface area. [My Copy] J Comput Chem (3 April 2007) by Georgy Rychkov, Michael Petukhov posted to protein solvation structure by BragilMassoud on 2007-04-07 12:36:36 as along with 3 people dgront mijam hryk
	Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein-Ligand Complexes. [My Copy] J Chem Inf Model (1 February 2007) by Yipin Lu, Renxiao Wang, Chao-Yie Y. Yang, Shaomeng Wang posted to structure protein hydration docking by BragilMassoud on 2007-02-04 14:59:12 as along with 2 people npt11tpn 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 structure protein nma by BragilMassoud on 2007-01-29 16:36:26 as along with 12 people and 7 groups ahmetbakan csrocha barry dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
	Protein structure comparison by alignment of distance matrices. [My Copy] Journal of molecular biology, Vol. 233, No. 1. (5 September 1993), pp. 123-138. by L. Holm, C. Sander posted to alignment protein structure by BragilMassoud on 2006-12-21 21:35:27 as along with 7 people and 2 groups jwm tjimenez ana nigham dgront siebertm sim82 structural_bioinformatics Bioinformatics
	Conformational Diversity of Ligands Bound to Proteins [My Copy] Journal of Molecular Biology, Vol. 356, No. 4. (3 March 2006), pp. 928-944. by Gareth R. Stockwell, Janet M. Thornton posted to conformation docking ligands protein structure by BragilMassoud on 2006-10-16 13:42:05 as along with 7 people JALumley ubcg08l apaydin kuhn bilab grottenolm thanatos
	Hierarchical and multi-resolution representation of protein flexibility. [My Copy] Bioinformatics (18 September 2006) by Yong Zhao, Daniel Stoffler, Michel Sanner posted to flexible_protein protein structure by BragilMassoud on 2006-09-22 17:09:10 as along with 4 people and 1 group dgruiz yongzhao kazemi LamBras TSRI_MGL
	Reduced surface: an efficient way to compute molecular surfaces. [My Copy] Biopolymers, Vol. 38, No. 3. (March 1996), pp. 305-320. by M. F. Sanner, A. J. Olson, J. C. Spehner posted to protein sasa structure visualization by BragilMassoud on 2006-08-30 16:20:02 as along with 4 people melo_mcr onufriev lillekatt sithmein
	The contour-buildup algorithm to calculate the analytical molecular surface. [My Copy] J Struct Biol, Vol. 116, No. 1. (b 1996), pp. 138-143. by M. Totrov, R. Abagyan posted to protein sasa structure visualization by BragilMassoud on 2006-08-30 16:18:28 as
	Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase. [My Copy] Proc Natl Acad Sci U S A, Vol. 90, No. 19. (1 October 1993), pp. 9031-9035. by M. Harel, I. Schalk, L. Ehret-Sabatier, et al.F. Bouet, M. Goeldner, C. Hirth, P. H. Axelsen, I. Silman, J. L. Sussman posted to 1acj bench_errors protein structure by BragilMassoud on 2006-07-22 19:59:18 as
	The Universal Protein Resource (UniProt): an expanding universe of protein information. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by C. H. Wu, R. Apweiler, A. Bairoch, et al.D. A. Natale, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M. J. Martin, R. Mazumder, C. O'Donovan, N. Redaschi, B. Suzek posted to db protein sequence by BragilMassoud on 2006-07-19 23:48:00 as along with 8 people niallhaslam sgoetz miguel anwazo dgront Haggan cdallett cjeans
	3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. [My Copy] Bioinformatics, Vol. 14, No. 2. (1998), pp. 188-195. by J. An, T. Nakama, Y. Kubota, A. Sarai posted to affinity db docking ligands protein structure by BragilMassoud on 2006-07-17 16:57:33 as
	Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures. [My Copy] Structure, Vol. 14, No. 6. (June 2006), pp. 967-972. by C. X. Weichenberger, M. J. Sippl posted to protein structure by BragilMassoud on 2006-07-12 20:45:12 as
	PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. [My Copy] Bioinformatics, Vol. 20, No. 6. (12 April 2004), pp. 986-988. by A. C. Martin posted to db protein structure by BragilMassoud on 2006-07-09 19:15:40 as
	Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas [My Copy] Journal of Computational Chemistry, Vol. 19, No. 7. (1998), pp. 797-808. by Jörg Weiser, Armin A. Weiser, Peter S. Shenkin, Clark W. Still posted to protein sasa structure visualization by BragilMassoud on 2006-06-28 21:42:44 as along with 1 person mijam
	Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 113-118. by A. Fernández, H. A. Scheraga posted to dehydron protein structure by BragilMassoud on 2006-06-15 23:07:09 as along with 3 people and 2 groups marti dkoveal barry structural_bioinformatics Bioinformatics
	Keeping dry and crossing membranes. [My Copy] Nat Biotechnol, Vol. 22, No. 9. (September 2004), pp. 1081-1084. by A. Fernández posted to dehydron protein review structure by BragilMassoud on 2006-06-01 14:41:27 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Incomplete protein packing as a selectivity filter in drug design. [My Copy] Structure, Vol. 13, No. 12. (December 2005), pp. 1829-1836. by A. Fernández posted to affinity dehydron ligands protein screening structure by BragilMassoud on 2006-06-01 14:30:24 as along with 1 person kuhn
	Molecular dimension explored in evolution to promote proteomic complexity. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 37. (14 September 2004), pp. 13460-13465. by A. Fernández, R. S. Berry posted to dehydron protein structure by BragilMassoud on 2006-06-01 14:30:01 as
	Dehydron: a structurally encoded signal for protein interaction. [My Copy] Biophys J, Vol. 85, No. 3. (September 2003), pp. 1914-1928. by A. Fernández, R. Scott posted to dehydron docking protein structure by BragilMassoud on 2006-05-28 13:03:00 as along with 4 people and 2 groups marti dkoveal barry Evangelia structural_bioinformatics Bioinformatics
	Evolutionary trace report maker: a new type of service for comparative analysis of proteins. [My Copy] Bioinformatics (27 April 2006) by I Mihalek, I Res, O Lichtarge posted to alignment evolution evotrace protein structure by BragilMassoud on 2006-04-30 15:10:21 as along with 1 person bilab
	Evolution of Hormone-Receptor Complexity by Molecular Exploitation [My Copy] Science, Vol. 312, No. 5770. (7 April 2006), pp. 97-101. by Jamie T. Bridgham, Sean M. Carroll, Joseph W. Thornton posted to evolution ligand protein structure by BragilMassoud on 2006-04-10 18:57:13 as along with 9 people and 2 groups wilbur Zephyrus psique anazhu86 kuhn imouthesmp xwbcn cmm jsnoddy R.E.A.D FAB-lab
	Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins. General recurrent equations [My Copy] Computers & Chemistry, Vol. 8, No. 4. (1984), pp. 239-247. by H. Abe, W. Braun, T. Noguti, N. Go posted to forcefield internal_coordinates math md protein by BragilMassoud on 2006-03-17 10:55:53 as
	How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations [My Copy] Science, Vol. 303, No. 5655. (9 January 2004), pp. 186-195. by Mireia Garcia-Viloca, Jiali Gao, Martin Karplus, Donald G. Truhlar posted to metabolomics nma protein structure by BragilMassoud on 2006-03-15 17:41:43 as along with 5 people mkrishna flbarroso baaden alexg tny
	Intrinsic dynamics of an enzyme underlies catalysis [My Copy] Nature, Vol. 438, No. 7064. (3 November 2005), pp. 117-121. by Elan Z. Eisenmesser, Oscar Millet, Wladimir Labeikovsky, et al.Dmitry M. Korzhnev, Magnus Wolf-Watz, Daryl A. Bosco, Jack J. Skalicky, Lewis E. Kay, Dorothee Kern posted to metabolomics nma protein structure by BragilMassoud on 2006-03-15 17:37:09 as along with 8 people mkrishna barry karbak lna dlr tny jlh64 rph
	Protein Folding: Computational Approaches to an Exponential-Time Problem [My Copy] Annual Review of Computer Science, Vol. 3 (1988), pp. 59-84. by George N. Reeke posted to forcefield minimization protein structure by BragilMassoud on 2006-03-12 17:12:04 as
	In quest of an empirical potential for protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (6 April 2006), pp. 166-171. by J. Skolnick posted to abinitio forcefield protein structure by BragilMassoud on 2006-03-12 15:00:19 as along with 4 people flbarroso krapnik nigham bilab
	Comparative modeling for protein structure prediction. [My Copy] Curr Opin Struct Biol (27 February 2006) by Krzysztof Ginalski posted to hom_model protein structure by BragilMassoud on 2006-03-09 13:54:51 as along with 8 people mijam mcbla kuhn rabio schuylrp ruvido insectopalo granujilla
	On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 4. (13 February 2006), pp. 892-906. by Murad Nayal, Barry Honig posted to cavities protein structure by BragilMassoud on 2006-02-19 14:20:26 as along with 6 people and 1 group ubcg08l iaolier pansapiens tjimenez Einat nickolay structural_bioinformatics
	Torsion angle dynamics for NMR structure calculation with the new program D? [My Copy] Journal of Molecular Biology, Vol. 273, No. 1. (17 October 1997), pp. 283-298. by P. Güntert posted to forcefield math md protein structure by BragilMassoud on 2006-02-14 17:36:18 as along with 5 people dsmueller ras stharward babakap lna
	Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement [My Copy] Proteins: Structure, Function, and Genetics, Vol. 19, No. 4. (August 1994), pp. 277-290. by Luke M. Rice, Axel T. Brünger posted to forcefield math md protein structure by BragilMassoud on 2006-02-14 17:29:46 as along with 1 person ras
	Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation [My Copy] Journal of Computational Chemistry, Vol. 15, No. 5. (1994), pp. 488-506. by Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov posted to docking forcefield math protein structure by BragilMassoud on 2006-02-13 22:03:36 as
	An alternative derivation of the equations of motion in torsion space for a branched linear chain. [My Copy] Protein Eng, Vol. 14, No. 11. (November 2001), pp. 825-828. by C. Bystroff posted to forcefield math protein structure by BragilMassoud on 2006-02-13 19:29:24 as
	Protein flexibility in ligand docking and virtual screening to protein kinases. [My Copy] J Mol Biol, Vol. 337, No. 1. (12 March 2004), pp. 209-225. by C. N. Cavasotto, R. A. Abagyan posted to docking kinases nma protein screening structure by BragilMassoud on 2006-02-11 15:07:05 as along with 9 people and 3 groups flbarroso oteri dgruiz yongzhao sangeetha anwazo daevans kazemi LamBras Bioinformatics TSRI_MGL insilicodrug
	Representing receptor flexibility in ligand docking through relevant normal modes. [My Copy] J Am Chem Soc, Vol. 127, No. 26. (6 July 2005), pp. 9632-9640. by C. N. Cavasotto, J. A. Kovacs, R. A. Abagyan posted to docking nma protein screening structure by BragilMassoud on 2006-02-11 14:26:34 as along with 6 people and 3 groups apaydin barry aqeel yongzhao kazemi LamBras structural_bioinformatics Bioinformatics TSRI_MGL
	Structural Evolution of the Protein Kinase-Like Superfamily. [My Copy] PLoS Comput Biol, Vol. 1, No. 5. (21 October 2005) by Eric D D. Scheeff, Philip E E. Bourne posted to alignment evolution kinases protein structure by BragilMassoud on 2006-01-24 14:55:54 as along with 4 people and 2 groups yuslinaz ana anwazo renatomilani structural_bioinformatics Bioinformatics
	Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 2. (1 January 2006), pp. 534-553. by Woody Sherman, Tyler Day, Matthew P. Jacobson, Richard A. Friesner, Ramy Farid posted to docking flexible_protein protein structure by BragilMassoud on 2006-01-21 16:53:47 as along with 7 people and 1 group klexa sschurer cen4ik LamBras yongzhao daevans kazemi TSRI_MGL
	MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. [My Copy] Protein Eng, Vol. 15, No. 12. (December 2002), pp. 959-965. by C. Bystroff posted to protein structure visualization by BragilMassoud on 2006-01-06 12:22:40 as along with 3 people saravan hryk dgront
	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
	Ribbon models of macromolecules [My Copy] J. Mol. Graph., Vol. 5, No. 2. (June 1987), pp. 103-106. by Mike Carson posted to protein ribbons structure visualization by BragilMassoud on 2005-12-23 21:39:32 as
	RIBBONS 2.0 [My Copy] Journal of Applied Crystallography, Vol. 24, No. 5. (1994), pp. 958-961. by M. Carson posted to protein ribbons structure visualization by BragilMassoud on 2005-12-23 21:31:58 as
	The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. [My Copy] PLoS Comput Biol, Vol. 1, No. 6. (18 November 2005) by Deqiang Zhang, J Andrew A. McCammon posted to nma protein structure by BragilMassoud on 2005-12-18 18:22:42 as along with 1 person saravan
	Multiple Alignment of protein structures and sequences for VMD. [My Copy] Bioinformatics (8 December 2005) by John Eargle, Dan Wright, Zaida Luthey-Schulten posted to alignment protein structure superposition visualization by BragilMassoud on 2005-12-17 13:37:27 as along with 2 people chad_davis kaarsinogen
	Coarse-grained normal mode analysis in structural biology [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 5. (October 2005), pp. 586-592. by Ivet Bahar, Aj Rader posted to nma protein structure by BragilMassoud on 2005-12-16 19:43:56 as along with 7 people and 2 groups apaydin barry aqeel shuns scis0000001 insectopalo higueruelo structural_bioinformatics Bioinformatics
	Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. [My Copy] Comput Chem, Vol. 19, No. 3. (September 1995), pp. 241-246. by D. Perahia, L. Mouawad posted to nma protein structure by BragilMassoud on 2005-12-13 20:57:08 as
	Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. [My Copy] J Mol Biol, Vol. 326, No. 2. (14 February 2003), pp. 485-492. by P. Chacón, F. Tama, W. Wriggers posted to nma protein structure by BragilMassoud on 2005-12-13 15:01:59 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
evotrace	4
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
sasa	3
textmining	3
abinitio	2
born	2
cancer	2
chemogenomics	2
consensus	2
database	2
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
fragments	1
framgents	1
geometry	1
ghb	1
glamdock	1
gpu	1
hammerhead	1
hbond	1
hom_model	1
hond	1
hydration	1
inverse_screening	1
kinase	1
language	1
ligandfit	1
loop_quantum	1
mechanics	1
metal	1
networks	1
neuro	1
open_access	1
openeye	1
optimization	1
pain	1
pdk1	1
pharmacolgy	1
pharmacologyy	1
psychedelics	1
psychology	1
qsar	1
qxp	1
random	1
rotation	1
rss	1
salvinorin	1
science	1
sequence	1
spline	1
therapy	1
water	1
xray	1

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