Referenzen:
-
N.N. Alexandrov, R. Nussinov, and R.M. Zimmer (1996)
Fast protein fold recognition via sequence to structure alignment and contact capacity potentials
In: Pacific Symposium on Biocomputing '96 (Lawrence Hunter & Teri E. Klein, Eds); World Scientific Publishing Co., Singapore, pp. 53-72
Threading (123D+)
-
Patrick Aloy, Matthieu Pichaud, and Robert B. Russell (2005)
Protein complexes: structure prediction challenges for the 21st century
Curr. Opin. Struct. Biol. 15: 15-22
Review
-
Herbert J. Bernstein (2000)
Recent changes to RasMol, recombining the variants
Trends Biochem. Sci. 25: 453-455
Visualisierung (RasMol)
-
R. Bonneau, C.E. Strauss, and D. Baker (2001)
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
Proteins 43: 1-11
ab initio Modelling (Rosetta)
-
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, and Leszek Rychlewski (2001)
LiveBench-1: continuous benchmarking of protein structure prediction servers
Protein Sci. 10: 352-361
Threading
-
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, and Leszek Rychlewski (2001)
LiveBench-2: large-scale automated evaluation of protein structure prediction servers
Proteins 45: 184-191
Threading
-
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, and Leszek Rychlewski (2001)
Structure prediction meta server
Bioinformatics 17: 750-751
Threading
-
C. Combet, M. Jambon, G. DelŽage, and C. Geourjon (2002)
Geno3D - an automated protein modeling Web server
Bioinformatics 18: 213-214
Homology Modelling (GENO3D)
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F.S. Domingues, W.A. Koppensteiner, M. Jaritz, A. Prlic, C. Weichenberger, M. Wiederstein, H. Floeckner, P. Lackner, and M.J. Sippl (1999)
Sustained performance of knowledge-based potentials in fold recognition
Proteins 37: 112-120
Threading (ProCeryon)
-
A. Elofsson, D. Fischer, D.W. Rice, S.M. Le Grand, and D. Eisenberg (1996)
A study of combined structure/sequence profiles
Fold Des. 1: 451-461
Threading (DOE Fold / FRSVR)
-
D. Fischer (2000)
Hybrid fold recognition: combining sequence derived properties with evolutionary information
In: Pacific Symposium on Biocomputing, Hawaii; World Scientific Publishing Co., Singapore, pp. 119-130
Threading (INBGU)
-
D. Fischer and D.A. Eisenberg (1996)
Protein fold recognition using sequence-derived predictions
Protein Sci. 5: 947-955
Threading (DOE Fold / FRSVR)
-
Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, and Leszek Rychlewski (2003)
3D-Jury: a simple approach to improve protein structure predictions
Bioinformatics 19: 1015-1018
Threading (Pcons)
-
Krzysztof Ginalski, Nick V. Grishin, Adam Godzik, and Leszek Rychlewski (2005)
Practical lessons from protein structure prediction
Nucleic Acids Res. 33: 1874-1891
Review
-
Nicolas Guex, Alexander Diemand, and Manuel C. Peitsch (1999)
Protein modelling for all
Trends Biochem. Sci. 24: 364-367
Homology Modelling (SWISS-MODEL)
-
Nicolas Guex and Manuel C. Peitsch (1997)
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling
Electrophoresis 18: 2714-2723
Visualisierung (Swiss-PdbViewer)
-
Jeanette Hargbo and Arne Elofsson (1999)
Hidden Markov models that use predicted secondary structures for fold recognition
Proteins 36: 68-76
Threading (ssHMM)
-
Christopher W.V. Hogue (1997)
Cn3D: a new generation of three-dimensional molecular structure viewer
Trends Biochem. Sci. 22: 314-316
Visualisierung (Cn3D)
-
Thomas Huber, Anthony J. Russell, Daniel Ayers, and Andrew E. Torda (1999)
Sausage: protein threading with flexible force fields
Bioinformatics 15: 1064-1065
Threading (Sausage)
-
D.T. Jones (1999)
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
J. Mol. Biol. 287: 797-815
Threading (genTHREADER)
-
D.T. Jones, W.R. Taylor and J.M. Thornton (1992)
A new approach to protein fold recognition
Nature 358: 86-89
Threading (THREADER)
-
D.T. Jones, M. Tress, K. Bryson, and C. Hadley (1999)
Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
Proteins 37: 104-111
Threading (THREADER)
-
Kevin Karplus, Christian Barrett and Richard Hughey (1998)
Hidden Markov models for detecting remote protein homologies
Bioinformatics 14: 846-556
Threading (SAM-T98)
-
K. Karplus, C. Barrett, M. Cline, M. Diekhans, L. Grate, and R. Hughey (1999)
Predicting protein structure using only sequence information
Proteins 37: 121-125
Threading (SAM-T98)
-
L.A. Kelley, R.M. MacCallum, and M.J.E. Sternberg (2000)
Enhanced genome annotation using structural profiles in the program 3D-PSSM
J. Mol. Biol. 299: 499-520
Threading (3D-PSSM)
-
David E. Kim, Dylan Chivian, and David Baker (2004)
Protein structure prediction and analysis using the Robetta server
Nucl. Acids Res. 32: W526-W531
ab initio Modelling (Robetta)
-
O. Lund, K. Frimand, J. Gorodkin, H. Bohr, J. Bohr, J. Hansen, and S. Brunak (1997)
Protein distance constraints predicted by neural networks and probability density functions
Protein Eng. 10: 1241-1248
Homology Modelling (CPHmodels)
-
Jesper Lundström, Leszek Rychlewski, Janusz Bujnicki, and Arne Elofsson (2001)
Pcons: a neural-network-based consensus predictor that improves fold recognition
Protein Sci. 10: 2354-2362
Threading (Pcons)
-
Jaroslaw Meller and Ron Elber (2001)
Linear programming optimization and a double statistical filter for protein threading protocols
Proteins 45: 241-261
Threading (LOOPP)
-
John Moult (2005)
A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
Curr. Opin. Struct. Biol. 15: 285-289
Review
-
A. Panchenko, A. Marchler-Bauer, and S.H. Bryant (1999)
Threading with explicit models for evolutionary conservation of structure and sequence
Proteins 37: 133-140
Threading
- Manuel C. Peitsch (1995)
Protein modelling by E-Mail
Bio/Technology 3: 658-660
Homology Modelling (SWISS-MODEL)
-
Manuel C. Peitsch, Timothy N.C. Wells, David R. Stampf, and Joel L. Sussman (1995)
The Swiss-3DImage collection and PDB-Browser on the World-Wide Web
Trends Biochem. Sci. 20: 82-84
Visualisierung (Swiss-3DImage)
-
Jan Reichert, Andreas Jabs, Peter Slickers, and Jürgen Sühnel (2000)
The IMB Jena Image Library of biological macromolecules
Nucleic Acids Res. 28: 246-249
Visualisierung (IMB Library)
-
David C. Richardson and Jane S. Richardson (1992)
The kinemage: a tool for scientific communication
Protein Sci. 1: 3-9
Visualisierung (Kinemage)
-
David C. Richardson and Jane S. Richardson (1994)
Kinemages - simple macromolecular graphics for interactive teaching and publication
Trends Biochem. Sci. 19: 135-138
Visualisierung (Kinemage)
-
Burkhard Rost (1995)
TOPITS: threading one-dimensional predictions into three-dimensional structures
Proc. Int. Conf. Intell. Syst. Mol. Biol. 3: 314-321
Threading (PHD TOPITS)
-
Burkhard Rost, Reinhard Schneider and Chris Sander (1997)
Protein fold recognition by prediction-based threading
J. Mol. Biol. 270: 471-480
Threading (PHD TOPITS)
-
R.B. Russell, M.A. Saqi, P.A. Bates, R.A. Sayle and M.J. Sternberg (1998)
Recognition of analogous and homologous protein folds--assessment of prediction success and associated alignment accuracy using empirical substitution matrices
Protein Eng. 11: 1-9
Threading (FoldFit)
-
Leszek Rychlewski and Daniel Fischer (2005)
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction
Protein Sci. 14: 240-245
Vergleich von 3D-Vorhersage-Servern
-
L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000)
Comparison of sequence profiles. Strategies for structural predictions using sequence information
Protein Sci. 9: 232-241
Threading (FFAS)
-
A. Sali and T.L. Blundell (1993)
Comparative protein modelling by satisfaction of spatial restraints
J. Mol. Biol. 234: 779-815
Molecular Modelling (MODELLER)
-
Roger A. Sayle and E. James Milner-White (1995)
RASMOL: biomolecular graphics for all
Trends Biochem. Sci. 20: 374-376
Visualisierung (RasMol)
-
J. Shi, T.L. Blundell and K. Mizugushi (2001)
Fugue: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
J. Mol. Biol. 310: 243-257
Threading (Fugue)
- I.N. Shindyalov and P.E. Bourne (2000)
Improving alignments in HM protocol with intermediate sequences
In: "Forth meeting on the critical assessment of techniques for protein structure prediction", p. A-92
Homology Modelling (SDSC1)
-
K.T. Simons, C. Kooperberg, E. Huang, and D. Baker (1997)
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
J. Mol. Biol. 268: 209-225
ab initio Modelling (Rosetta)
-
K.T. Simons, R. Bonneau, I. Ruczinski, and D. Baker (1999)
Ab initio protein structure prediction of CASP III targets using ROSETTA
Proteins Suppl 3: 171-176
ab initio Modelling (Rosetta)
-
Charles W. Sokolik (1995)
Kinemages: make your own molecules for teaching
Trends Biochem Sci. 20: 122-124
Visualisierung (Kinemage)
-
David R. Stampf, Clifford E. Felder, and Joel L. Sussman (1995)
PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank
Nature 374: 572-574
Visualisierung (PDBBrowse)
-
Rosemarie Swanson and Jerry Tsai (2003)
Pretty good guessing: protein structure prediction at CASP5
J. Bacteriol. 185: 3990-3993
Review
-
Gerrit Vriend (1990)
WHAT IF: a molecular modeling and drug design program
J. Mol. Graph. 8: 52-56
Molecular Modelling (WHAT IF)
-
Dirk Walther (1997)
WebMol - a Java based PDB viewer
Trends Biochem. Sci. 22: 274-275
Visualisierung (WebMol)
-
Yanli Wang, Lewis Y. Geer, Colombe Chappey, Jonathan A. Kans, and Stephen H. Bryant (2000)
Cn3D: sequence and structure views for Entrez
Trends Biochem. Sci. 25: 300-302
Visualisierung (Cn3D)
-
Ying Xu and Dong Xu (2000)
Protein threading using PROSPECT: design and evaluation
Proteins 40: 343-354
Threading (PROSPECT)
Latest update of content: October 4, 2005
Ralf Koebnik
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