Improving the Performance of Rosetta Using Multiple Sequence Alignment Information and Global Measures of Hydrophobic Core Formation

Improving the Performance of Rosetta Using Multiple Sequence Alignment Information and Global Measures of Hydrophobic Core Formation (2001)

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by Richard Bonneau , Charlie Strauss , David Baker

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22 - 14 self

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@MISC{Bonneau01improvingthe,
    author = {Richard Bonneau and Charlie Strauss and David Baker},
    title = {Improving the Performance of Rosetta Using Multiple Sequence Alignment Information and Global Measures of Hydrophobic Core Formation},
    year = {2001}
}

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Abstract

Thisstudyexplorestheuseofmultiplesequencealignment (MSA)informationand globalmeasuresofhydrophobiccoreformationfor improvingtheRosettaabinitioproteinstructure predictionmethod.Themosteffectiveuseofthe MSAinformationisachievedbycarryingoutindependentfoldingsimulationsforasubsetofthe homologoussequencesintheMSAandthenidentifyingthefreeenergyminimacommontoallfolded sequencesviasimultaneousclusteringoftheindependentfoldingruns. Globalmeasuresofhydrophobiccoreformation, usingellipsoidalratherthan sphericalrepresentationsofthehydrophobiccore, arefoundtobeusefulinremovingnon-nativeconformationsbeforeclusteranalysis. ThroughthiscombinationofMSAinformationandglobalmeasuresof proteincoreformation,wesignificantlyincrease theperformanceofRosettaonachallengingtestset. Proteins2001;43:1--11.2001Wiley-Liss,Inc.

Citations

1150	DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res - SF, TL, et al. - 1997
338	C: Prediction of protein secondary structure at better than 70% accuracy - Rost, Sander - 1993
190	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions - Simons, Kooperberg, et al. - 1997
172	Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56–68 - Sander, Schneider - 1991
109	Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins (Supplement 3 - Simons, Bonneau, et al. - 1999
51	Protein secondary structure prediction based on positionspecific scoring matrices - DT - 1999
47	D: Clustering of low-energy conformations near the native structures of small proteins - Shortle, KT, et al. - 1998
34	Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D: Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins - KT - 1999
29	PR: Weighting in sequence space: a comparison of methods in terms of generalized sequences - Vingron, Sibbald - 1993
18	Factors affecting the ability of energy functions to discriminate correct from incorrect folds - BH, ES, et al. - 1997
17	A structural explanation for the twilight zone of protein sequence homology - Chung, Subbiah - 1996
17	MJ: Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci - RD, Sternberg - 1996
11	Do aligned sequences share the same fold - RA, Batalov - 1997
11	An evolutionary approach to folding small �-helical proteins that uses sequence information and an empirical guiding fitness function - JU, Eisenberg
9	Fidelis K, Pedersen JT. Critical assessment of methods of protein structure prediction (CASP): round III. Proteins 1999;Suppl 3:2–6 - Moult, Hubbard
9	Knowledge-based potentials for proteins. Curr Opin Struct Biol - MJ - 1995
7	Zemla A, Fidelis K, Moult J. Some measures of comparative performance - Venclovas
7	Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set - VA, DM, et al. - 1999
7	Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symp Biocomput - Samudrala, Xia, et al. - 1999
7	Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships - SE - 1998
7	Additivity principles in biochemistry - KA - 1997
6	Wolynes PG. Intermediates and barrier crossing in a random energy model - JD - 1989
6	C: MView: A Web compatible database search or multiple alignment viewer. Bioinformatics - NP, Leroy, et al. - 1998
5	Gunsteren WF. Decomposition of the free energy of a system in terms of specific interactions - AE, van - 1994
4	Finkelstein AV. Averaging interaction energies over homologs improves protein fold recognition in gapless threading. Proteins - BA, Skolnick - 1999
4	AC, Lo Conte L, Thornton JM. The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res 1999;27:275 - CA, FM, et al.
2	How homologs can help to predict protein folds even though they cannot be predicted for individual sequences - Badretdinov, AV - 1998
2	Coupling the folding of homologous proteins - Keasar, Tobi, et al.
2	The HSSP data base of protein structure– sequence alignments. Nucleic Acids Res - Sander, Schneider - 1993
1	Recognizing native folds by the of hydrophobic and polar residues - ES, Subbiah, et al. - 1995