kgutwin's predictions [75 articles] Export

Recent papers added to kgutwin's library classified by the tag predictions. You can also see everyone's predictions.

	Prediction and integration of regulatory and protein-protein interactions. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 541 (2009), pp. 101-143. by Duangdao Wichadakul, Jason McDermott, Ram Samudrala posted to interactions litreview2009 predictions by kgutwin on 2009-08-05 23:00:20 as
	Prediction of protein-protein interactions: a study of the co-evolution model. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 541 (2009), pp. 61-88. by Itai Sharon, Jason V. Davis, Golan Yona posted to interactions litreview2009 predictions by kgutwin on 2009-08-05 23:00:04 as along with 3 people chica zwang phoenixzxl
	Inferring protein-protein interactions from multiple protein domain combinations. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 541 (2009), pp. 43-59. by Simon P. Kanaan, Chengbang Huang, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre posted to interactions litreview2009 predictions by kgutwin on 2009-08-05 22:59:45 as along with 1 person zwang
	Complex discovery from weighted PPI networks. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1891-1897. by Guimei Liu, Limsoon Wong, Hon Nian N. Chua posted to complex litreview2009 predictions by kgutwin on 2009-08-05 22:58:55 as along with 7 people kiekyon zwang friendpine poirel neils tmmurali grahamc
	Computational prediction of protein-protein interactions. [My Copy] Molecular biotechnology, Vol. 38, No. 1. (20 January 2008), pp. 1-17. by Lucy Skrabanek, Harpreet K. Saini, Gary D. Bader, Anton J. Enright posted to interactions litreview2009 predictions by kgutwin on 2009-08-05 22:57:24 as along with 7 people iris_2001 jperkins kiekyon jwhitney ruvido guhjy penpen926
	When a predicted coiled coil is really a single [small alpha]-helix, in myosins and other proteins [My Copy] Soft Matter, Vol. 5, No. 13. (2009), pp. 2493-2503. by Michelle Peckham, Peter J. Knight posted to litreview2009 myosin predictions single-alpha-helix by kgutwin on 2009-08-05 21:52:55 as along with 1 person melting
	Template-based modeling and free modeling by I-TASSER in CASP7 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 108-117. by Yang Zhang posted to casp post-defense predictions structure tasser ab-initio by kgutwin on 2009-05-20 07:39:31 as
	Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. [My Copy] Proteins, Vol. 69, No. S8. (25 September 2007), pp. 118-128. by Rhiju Das, Bin Qian, Srivatsan Raman, et al.Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D D. Tyka, Divya Bhat, Dylan Chivian, David E E. Kim, William H H. Sheffler, Lars Malmström, Andrew M M. Wollacott, Chu Wang, Ingemar Andre, David Baker posted to casp post-defense predictions rosetta structure ab-initio by kgutwin on 2009-05-20 07:37:22 as along with 3 people mcbla jwm Ema
	KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. [My Copy] Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007) by Y. H. Wong, T. Y. Lee, H. K. Liang, et al.C. M. Huang, T. Y. Wang, Y. H. Yang, C. H. Chu, H. D. Huang, M. T. Ko, J. K. Hwang posted to kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:16:33 as along with 1 person guhjy
	Kinase-specific prediction of protein phosphorylation sites. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 527 (2009) by Martin L. Miller, Nikolaj Blom posted to kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:16:14 as along with 3 people guhjy niallhaslam hryk
	Substrate specificity of protein kinases and computational prediction of substrates. [My Copy] Biochim Biophys Acta, Vol. 1754, No. 1-2. (30 December 2005), pp. 200-209. by B. Kobe, T. Kampmann, J. K. Forwood, P. Listwan, R. I. Brinkworth posted to domains kinase post-defense predictions specificity by kgutwin on 2009-05-20 07:06:52 as
	Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains [My Copy] Mol Cell Proteomics (20 November 2008), M800450-MCP200. by Tingjun Hou, Zheng Xu, Wei Zhang, et al.William A. Mclaughlin, David A. Case, Yang Xu, Wei Wang posted to domains post-defense predictions sh3 by kgutwin on 2009-05-20 05:41:36 as along with 2 people phoenixzxl zwang
	Structure Based Prediction of the S. cerevisiae SH3-Ligand Interactions. [My Copy] Journal of molecular biology (23 March 2009) by Gregorio Fernandez-Ballester, Pedro Beltrao, Jose Manuel M. Gonzalez, et al.Young-Hwa H. Song, Matthias Wilmanns, Alfonso Valencia, Luis Serrano posted to domains ism post-defense predictions sh3 by kgutwin on 2009-05-20 05:41:04 as along with 1 person neils
	Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. [My Copy] Nucleic acids research, Vol. 36, No. 10. (June 2008), pp. 3263-3273. by L. Li, C. Wu, H. Huang, K. Zhang, J. Gan, S. S. Li posted to domains post-defense predictions sh2 by kgutwin on 2009-05-20 05:40:08 as along with 1 person hryk
	A Specificity Map for the PDZ Domain Family [My Copy] PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239. by Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, et al.Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A. Held, Brent A. Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C. Chan, Somasekar Seshagiri, Laurence A. Lasky, Chris Sander, Charles Boone, Gary D. Bader, Sachdev S. Sidhu posted to domains pdz post-defense predictions by kgutwin on 2009-05-20 05:37:28 as along with 6 people and 3 groups balicea grahamc markchen zwang cabbagesofdoom barry structural_bioinformatics McCammon Bioinformatics
	Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. [My Copy] Journal of molecular biology, Vol. 343, No. 3. (22 October 2004), pp. 703-718. by U. Wiedemann, P. Boisguerin, R. Leben, et al.D. Leitner, G. Krause, K. Moelling, R. Volkmer-Engert, H. Oschkinat posted to domains pdz post-defense predictions spot-array by kgutwin on 2009-05-20 05:37:05 as
	The limits of protein secondary structure prediction accuracy from multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 234, No. 4. (20 December 1993), pp. 951-957. by R. B. Russell, G. J. Barton posted to post-defense predictions secondary-structure by kgutwin on 2009-05-20 02:32:34 as
	Effective energy functions for protein structure prediction [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 139-145. by T. Lazaridis posted to design post-defense predictions statpot by kgutwin on 2009-05-19 19:19:12 as along with 2 people ckmyo flbarroso
	Interrogating protein interaction networks through structural biology [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901. by Patrick Aloy, Robert B. Russell posted to interactions interprets predictions statpot post-defense by kgutwin on 2009-05-19 19:02:58 as along with 15 people and 3 groups beete aceol tomhebbron bpcusack ana barry baaden bicko lfriedl chad_davis henschel ruvido cjeans tale Evangelia structural_bioinformatics kdl Bioinformatics
	InterPreTS: protein interaction prediction through tertiary structure. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 161-162. by P. Aloy, R. B. Russell posted to interactions interprets predictions statpot structure post-defense by kgutwin on 2009-05-19 18:52:27 as along with 6 people baaden bicko chad_davis henschel ruvido Pao-Yang
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to design post-defense predictions rosetta structure by kgutwin on 2009-05-19 04:23:35 as along with 10 people bmduggan Diego_Prada onufriev apaydin dfgreen jwm hmk heymiki kevinchannon ca3295
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to ab-initio post-defense predictions rosetta structure by kgutwin on 2009-05-19 04:17:00 as along with 11 people and 4 groups ucbcjbm paddydu BragilMassoud ana barry thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Fold prediction of helical proteins using torsion angle dynamics and predicted restraints [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 6. (19 March 2002), pp. 3581-3585. by Chao Zhang, Jingtong Hou, Sung-Hou Kim posted to helix-packing post-defense predictions by kgutwin on 2009-05-17 02:36:33 as
	Packing helices in proteins by global optimization of a potential energy function. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 4. (18 February 2003), pp. 1706-1710. by M. Nanias, M. Chinchio, J. Pillardy, D. R. Ripoll, H. A. Scheraga posted to helix-packing post-defense predictions by kgutwin on 2009-05-17 02:35:40 as along with 1 person pansapiens
	A computational pathway for bracketing native-like structures for small alpha helical globular proteins [My Copy] Phys. Chem. Chem. Phys., Vol. 7, No. 11. (2005), pp. 2364-2375. by Pooja Narang, Kumkum Bhushan, Surojit Bose, B. Jayaram posted to helix-packing need-pdf post-defense predictions by kgutwin on 2009-05-17 02:33:14 as
	Iterative assembly of helical proteins by optimal hydrophobic packing. [My Copy] Structure (London, England : 1993), Vol. 16, No. 8. (August 2008), pp. 1257-1266. by G. A. Wu, E. A. Coutsias, K. A. Dill posted to helix-packing post-defense predictions structure by kgutwin on 2009-05-17 02:21:49 as
	Prediction of Protein Secondary Structure at Better than 70% Accuracy [My Copy] Journal of Molecular Biology, Vol. 232, No. 2. (20 July 1993), pp. 584-599. by Burkhard Rost, Chris Sander posted to post-defense predictions secondary-structure by kgutwin on 2009-05-17 02:08:15 as along with 2 people svozil chad_davis
	Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins [My Copy] Journal of Molecular Biology, Vol. 120, No. 1. (25 March 1978), pp. 97-120. by J. Garnier, D. Osguthorpe, B. Robson posted to gor need-pdf post-defense predictions secondary-structure by kgutwin on 2009-05-17 02:04:02 as
	Protein secondary structure prediction based on position-specific scoring matrices. [My Copy] Journal of molecular biology, Vol. 292, No. 2. (17 September 1999), pp. 195-202. by D. T. Jones posted to post-defense predictions psipred secondary-structure by kgutwin on 2009-05-17 02:03:33 as along with 11 people rpetrenko pjcite chad_davis wouterboomsma j3xucite dgront rabio rph dandaman saunders granujilla
	[32] GOR method for predicting protein secondary structure from amino acid sequence [My Copy] In Computer Methods for Macromolecular Sequence Analysis, Vol. 266 (1996), pp. 540-553. by J. Garnier, J. Gibrat, B. Robson posted to gor post-defense predictions secondary-structure by kgutwin on 2009-05-17 02:02:19 as
	Prediction of protein conformation. [My Copy] Biochemistry, Vol. 13, No. 2. (15 January 1974), pp. 222-245. by P. Y. Chou, G. D. Fasman posted to chou-fasman need-pdf predictions secondary-structure post-defense by kgutwin on 2009-05-17 00:39:48 as
	The Chou-Fasman secondary structure prediction method with an extended data base. [My Copy] FEBS letters, Vol. 93, No. 1. (1 September 1978), pp. 19-24. by P. Argos, M. Hanei, R. M. Garavito posted to chou-fasman database post-defense predictions secondary-structure by kgutwin on 2009-05-17 00:38:21 as
	Prediction of the secondary structure of proteins from their amino acid sequence. [My Copy] Adv Enzymol Relat Areas Mol Biol, Vol. 47 (1978), pp. 45-148. by P. Y. Chou, G. D. Fasman posted to need-pdf chou-fasman predictions secondary-structure post-defense by kgutwin on 2009-05-17 00:37:06 as
	Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins. [My Copy] Journal of molecular biology, Vol. 88, No. 4. (5 October 1974), pp. 873-894. by V. I. Lim posted to post-defense predictions secondary-structure by kgutwin on 2009-05-17 00:34:28 as
	Coiled coil structures and transcription: an analysis of the S. cerevisiae coilome. [My Copy] Mol Genet Genomics (3 May 2007) by Kellie E. Barbara, Kristine A. Willis, Terry M. Haley, Stephen J. Deminoff, George M. Santangelo posted to coiled-coils genome newcoils paircoil predictions by kgutwin on 2009-05-06 21:12:24 as along with 2 people cjeans chgjb
	Dynamitin Mutagenesis Reveals ProteinProtein Interactions Important for Dynactin Structure [My Copy] Traffic, Vol. 9, No. 4. (April 2008), pp. 481-491. by Maier, C. Kerstin, Godfrey, et al.E. Jamie, Echeverri, J. Christophe, Cheong, K. Y. Frances, Schroer, A. Trina posted to coiled-coils multicoil spectrin trimer predictions by kgutwin on 2009-05-06 20:28:47 as
	Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: comparison to the X-ray structure. [My Copy] Proteins, Vol. 15, No. 2. (February 1993), pp. 133-146. by M. Nilges, A. T. Brünger posted to bzip coiled-coils modeling structure predictions by kgutwin on 2009-05-06 15:49:19 as along with 1 person hplatero
	Automated modeling of coiled coils: application to the GCN4 dimerization region. [My Copy] Protein Eng, Vol. 4, No. 6. (August 1991), pp. 649-659. by M. Nilges, A. T. Brünger posted to coiled-coils modeling predictions by kgutwin on 2009-05-06 15:48:16 as along with 2 people oteri hplatero
	Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks. [My Copy] Mol Biol Evol, Vol. 23, No. 8. (August 2006), pp. 1480-1492. by C. D. Deppmann, R. S. Alvania, E. J. Taparowsky posted to bzip interactions review predictions by kgutwin on 2009-04-30 04:39:56 as along with 3 people cjeans hplatero gwenknight
	Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure1 [My Copy] Journal of Molecular Biology, Vol. 306, No. 3. (23 February 2001), pp. 607-628. by Hidetoshi Kono, Jeffery G. Saven posted to modeling predictions by kgutwin on 2009-04-27 04:49:02 as along with 3 people jwm dfgreen blackbart
	Predicting protein-protein interactions from primary structure [My Copy] Bioinformatics, Vol. 17, No. 5. (1 May 2001), pp. 455-460. by Joel R. Bock, David A. Gough posted to interactions svm predictions by kgutwin on 2009-04-24 03:12:19 as along with 7 people renatomilani joseolucha maryee cjeans Evangelia iris_2001 wilbur
	Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. [My Copy] Genes & development, Vol. 7, No. 6. (June 1993), pp. 1047-1058. by C. R. Vinson, T. Hai, S. M. Boyd posted to bzip coiled-coils rational-model residue-preferences predictions by kgutwin on 2009-04-23 20:36:58 as
	Sequence-based feature prediction and annotation of proteins. [My Copy] Genome biology, Vol. 10, No. 2. (2 February 2009) by Agnieszka S. Juncker, Lars J. Jensen, Andrea Pierleoni, et al.Andreas Bernsel, Michael L. Tress, Peer Bork, Gunnar von Heijne, Alfonso Valencia, Christos A. Ouzounis, Rita Casadio, Søren Brunak posted to review sequence predictions by kgutwin on 2009-04-22 23:16:40 as along with 5 people larsjuhljensen nyyu shwu neils druvus
	Repacking protein cores with backbone freedom: structure prediction for coiled coils. [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 18. (29 August 1995), pp. 8408-8412. by P. B. Harbury, B. Tidor, P. S. Kim posted to coiled-coils crick-param modeling predictions structure by kgutwin on 2009-04-22 22:50:22 as along with 3 people oteri dfgreen bethbromley
	Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 24. (13 June 2006), pp. 8989-8994. by J. M. Mason, M. A. Schmitz, K. M. Müller, K. M. Arndt posted to bzip design rational-model residue-preferences predictions by kgutwin on 2009-04-22 18:22:52 as along with 4 people gwenknight chgjb bethbromley ca3295
	Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils [My Copy] Proc Natl Acad Sci U S A, Vol. 98, No. 26. (Dec 2001), pp. 14825-14830. by A. E. Keating, V. N. Malashkevich, B. Tidor, P. S. Kim posted to coiled-coils keating-import predictions by kgutwin on 2009-04-08 21:33:50 as
	An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. [My Copy] Bioinformatics (Oxford, England), Vol. 18, No. 4. (April 2002), pp. 617-625. by Mauro Delorenzi, Terry Speed posted to coiled-coils hmm marcoil predictions by kgutwin on 2009-03-19 01:38:54 as along with 6 people TLVincent oteri hansen cjeans gwenknight ca3295
	Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper. [My Copy] Proteins, Vol. 35, No. 4. (1 June 1999), pp. 447-452. by D. Mohanty, B. N. Dominy, A. Kolinski, C. L. Brooks, J. Skolnick posted to predictions lattice-model bzip statpot structure by kgutwin on 2009-03-19 01:08:24 as
	Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometries. [My Copy] Folding & design, Vol. 2, No. 4. (1997) by S. I. O'Donoghue, M. Nilges posted to bzip esm need-pdf potential structure predictions by kgutwin on 2009-03-19 01:07:19 as
	Computational approaches to identify leucine zippers. [My Copy] Nucleic acids research, Vol. 26, No. 11. (1 June 1998), pp. 2740-2746. by E. Bornberg-Bauer, E. Rivals, M. Vingron posted to predictions bzip newcoils by kgutwin on 2009-03-19 01:04:52 as

Note: You may cite this page as: http://www.citeulike.org/user/kgutwin/tag/predictions

Result page: 1 2 Next

coiled-coils	138
predictions	75
post-defense	70
structure	64
bzip	41
statpot	37
review	33
trimer	33
interactions	30
historical	27
antiparallel	23
newfams-evidence	21
design	20
tropomyosin	17
residue-preferences	17
keating-import	16
dimer	16
litreview2008	16
oakley-import	15
database	13
analysis	13
trigger-sequence	12
domains	12
need-pdf	11
potential	11
secondary-structure	10
expt-evidence	10
helix-packing	9
specificity	9
litreview2009	9
crick-param	8
ori-dep-potential	8
multicoil	8
paircoil	8
rosetta	8
coupling-energy	8
docking	8
modeling	7
myosin	7
electrostatics	7
dfire	7
alignment	7
threading	6
socket	6
nemo	6
kinase	6
folding	6
snare	6
keratin	6
reference-state	6
svm	5
newcoils	5
ab-initio	5
genome	5
families	5
zincfinger	4
ism	4
chou-fasman	4
homodimer	4
collagen	4
interfaces	4
scaffold	3
tpr	3
molecular-mechanics	3
laminin	3
cluster-expansion	3
sh3	3
tenascin	3
reduced	3
miyazawa-jernigan	3
fiber-diffraction	3
multiprospector	3
contact	3
sequence	3
homologs	3
sindbis-virus	3
tetramer	3
marcoil	3
profiles	3
hemagglutinin	3
learncoil	3
right-handed	3
correlations	3
pdz	3
heterodimer	3
gor	2
spc110p	2
hmm	2
hsfbp1	2
electron-microscopy	2
multiprot	2
chemistry	2
single-alpha-helix	2
mlp	2
blast	2
campbd	2
kinetics	2
opus	2
charmm	2
fibrinogen	2
short	2
tasser	2
interprets	2
theoretical	2
astrin	2
npc	2
rational-model	2
motions	2
spb	2
lattice-model	2
spectrin	2
sh2	2
knobs-into-holes	2
casp	2
dope	2
numa	2
prediction	2
spot-array	1
model-forms	1
information-theory	1
ser-rs	1
calmodulin	1
fer	1
atpase	1
divergence	1
clustering	1
homology-model	1
uniref	1
yeast-2-hybrid	1
vbp	1
l1orf1	1
hsf	1
lattice	1
smc	1
classy	1
clashes	1
orientation	1
p-het	1
clpb	1
psipred	1
substitution-matrix	1
amber	1
chromophore	1
fusion	1
residue-composition	1
pqs	1
ramachandran	1
cortexillin	1
gp41	1
fractal	1
snv_n	1
systers	1
hairpin	1
tsp1	1
hydrogen-bond	1
foldx	1
esm	1
complex	1
eef1	1
structure-aln	1
hpc	1
solvent	1
brca1	1
arabidopsis	1
dynein	1
matrilin	1
genbank	1
intramolecular	1
dna	1
binding	1
predicted-cc	1
microarray	1
functions	1
rop	1
biojava	1
heptad-shift	1
minimization	1
ultra-high-xtal	1
all-atom	1
ef-hand	1
scop	1
rna	1

kgutwin's predictions [75 articles] Export

kgutwin's tags