Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker  Home/Search
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Abstract: We describe the development of a scoring function based on the decomposition P(structure 0 sequence) ~ P(sequence structure) *P(structure), which outperforms previous scoring functions in correctly identifying native-like protein structures in large ensembles of compact decoys. The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the assembly of... (Update)
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BibTeX entry: (Update)
Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystro# C, Baker D. Improved recognition of nativelike protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82--95. http://citeseer.ist.psu.edu/kt99improved.html More
@misc{ kt99improved,
author = "S. KT and R. Kooperberg and C. Fox and B. Bystro and C. Baker",
title = "Improved recognition of nativelike protein structures using a combination
of sequence-dependent and sequence-independent features of proteins",
text = "Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystro# C, Baker D. Improved
recognition of nativelike protein structures using a combination of sequence-dependent
and sequence-independent features of proteins. Proteins 1999;34:82--95.",
year = "1999",
url = "citeseer.ist.psu.edu/kt99improved.html" }
Citations (may not include all citations):162 The Protein Data Bank: a computer-based archival file for ma.. (context) - FC, TF et al. - 1977
70 A method to identify protein sequences that fold into a know.. (context) - JU, Eisenberg - 1991
44 Combining probability distributions: a critique and an annot.. (context) - Genest, Zidek - 1986
33 Enlarged representative set of protein structures (context) - Hobohm, Sander - 1994
32 Calculation of conformational ensembles from potentials of m.. (context) - MJ - 1990
28 Assembly of protein tertiary structures from fragments with .. - KT, Huang et al. - 1997
20 Energy functions that discriminate x-ray and near-native fol.. - Park, Levitt - 1996
19 An all-atom distance dependent conditional probability discr.. (context) - Samudrala, Moult - 1998
19 Residue-residue potentials with a favorable contact pair ter.. - Miyazawa - 1996
18 Monte Carlo simulations of protein folding (context) - Kolinski, Skolnick - 1994
16 Factors affecting the ability of energy functions to discrim.. - BH, ES - 1997
13 Factors influencing the ability of knowledge-based potential.. (context) - JA, MJ et al. - 1994
10 LINUS: a hierarchic procedure to predict the fold of a prote.. (context) - Srinivasan - 1995
9 Database algorithm for generating protein backbone and side-.. (context) - Holm, Sander - 1991
6 Identifying the tertiary fold of small proteins with differe.. (context) - Dandekar, Argos - 1996
6 Prediction of local structure in proteins using a library of.. - Bystroff, Baker - 1998
4 Using a hydrophobic contact potential to evaluate native and.. - ES, Tsai et al. - 1996
4 Coordination geometry of nonbonded residues in globular prot.. (context) - Bahar - 1996
4 Computer modeling of protein folding: conformational and ene.. (context) - Monge - 1995
2 A novel super-secondary structure of proteins and the relati.. (context) - AV - 1984
2 Packing of secondary structural elements in proteins (context) - BVB, TL - 1993
2 Principles of helix-helix packing in proteins: the helical l.. (context) - Walther, Eisenhaber et al. - 1996
1 Helix packing angle preferences (context) - JU - 1997
1 side-chain packing: the distribution of interplanar angles (context) - JBO, RA et al. - 1996
1 Rebuilding flavodoxin from C alpha coordinates: a test study (context) - LS, JM - 1989
1 Adv Protein Chem (context) - JS, taxonomy et al. - 1981
1 Four helix bundle diversity in globular proteins (context) - NL, SR et al. - 1994
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