Publications
-
Insights into the intra-ring subunit order of tric/cct: a structural and evolutionary analysis.
Kalisman N,
Levitt M.
Pac Symp Biocomput.
2010:
252-9
-
Protein segment finder: an online search engine for segment motifs in the PDB.
Samson AO,
Levitt M.
Nucleic Acids Res.
2009;
37
(Database issue):
D224-8
-
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
Wang D,
Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD.
Science.
2009;
324
(5931):
1203-6
-
Nature of the protein universe.
Levitt M,
Proc Natl Acad Sci U S A.
2009;
106
(27):
11079-84
-
How hydrophobic buckminsterfullerene affects surrounding water structure.
Weiss DR,
Raschke TM, Levitt M.
J Phys Chem B.
2008;
112
(10):
2981-90
-
Probing protein fold space with a simplified model.
Minary P,
Levitt M.
J Mol Biol.
2008;
375
(4):
920-33
-
Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability.
Sykes MT,
Levitt M.
Proc Natl Acad Sci U S A.
2007;
104
(30):
12336-40
-
Near-native structure refinement using in vacuo energy minimization.
Summa CM,
Levitt M.
Proc Natl Acad Sci U S A.
2007;
104
(9):
3177-82
-
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.
Schröder GF,
Brunger AT, Levitt M.
Structure.
2007;
15
(12):
1630-41
-
Growth of novel protein structural data.
Levitt M,
Proc Natl Acad Sci U S A.
2007;
104
(9):
3183-8
-
Spatial regulation and the rate of signal transduction activation.
Batada NN,
Shepp LA, Siegmund DO, Levitt M.
PLoS Comput Biol.
2006;
2
(5):
e44
-
Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them.
Raschke TM,
Levitt M.
Proc Natl Acad Sci U S A.
2005;
102
(19):
6777-82
-
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.
Kolodny R,
Koehl P, Levitt M.
J Mol Biol.
2005;
346
(4):
1173-88
-
An atomic environment potential for use in protein structure prediction.
Summa CM,
Levitt M, Degrado WF.
J Mol Biol.
2005;
352
(4):
986-1001
-
Describing RNA structure by libraries of clustered nucleotide doublets.
Sykes MT,
Levitt M.
J Mol Biol.
2005;
351
(1):
26-38
-
Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.
Batada NN,
Westover KD, Bushnell DA, Levitt M, Kornberg RD.
Proc Natl Acad Sci U S A.
2004;
101
(50):
17361-4
-
Protein decoy assembly using short fragments under geometric constraints.
Kolodny R,
Levitt M.
Biopolymers.
2003;
68
(3):
278-85
-
Funnel sculpting for in silico assembly of secondary structure elements of proteins.
Fain B,
Levitt M.
Proc Natl Acad Sci U S A.
2003;
100
(19):
10700-5
-
A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics.
Keasar C,
Levitt M.
J Mol Biol.
2003;
329
(1):
159-74
-
Design of an optimal Chebyshev-expanded discrimination function for globular proteins.
Fain B,
Xia Y, Levitt M.
Protein Sci.
2002;
11
(8):
2010-21
-
Improved recognition of native-like protein structures using a family of designed sequences.
Koehl P,
Levitt M.
Proc Natl Acad Sci U S A.
2002;
99
(2):
691-6
-
Protein topology and stability define the space of allowed sequences.
Koehl P,
Levitt M.
Proc Natl Acad Sci U S A.
2002;
99
(3):
1280-5
-
Small libraries of protein fragments model native protein structures accurately.
Kolodny R,
Koehl P, Guibas L, Levitt M.
J Mol Biol.
2002;
323
(2):
297-307
-
Sequence variations within protein families are linearly related to structural variations.
Koehl P,
Levitt M.
J Mol Biol.
2002;
323
(3):
551-62
-
Roles of mutation and recombination in the evolution of protein thermodynamics.
Xia Y,
Levitt M.
Proc Natl Acad Sci U S A.
2002;
99
(16):
10382-7
-
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.
Yona G,
Levitt M.
J Mol Biol.
2002;
315
(5):
1257-75
-
The birth of computational structural biology.
Levitt M,
Nat Struct Biol.
2001;
8
(5):
392-3
-
Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water.
Raschke TM,
Tsai J, Levitt M.
Proc Natl Acad Sci U S A.
2001;
98
(11):
5965-9
-
A novel method for sampling alpha-helical protein backbones.
Fain B,
Levitt M.
J Mol Biol.
2001;
305
(2):
191-201
-
The ASTRAL compendium for protein structure and sequence analysis.
Brenner SE,
Koehl P, Levitt M.
Nucleic Acids Res.
2000;
28
(1):
254-6
-
Ab initio construction of protein tertiary structures using a hierarchical approach.
Xia Y,
Huang ES, Levitt M, Samudrala R.
J Mol Biol.
2000;
300
(1):
171-85
-
Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins.
Yona G,
Levitt M.
Proc Int Conf Intell Syst Mol Biol.
2000:
8
395-406
-
Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction.
Samudrala R,
Levitt M.
Protein Sci.
2000;
9
(7):
1399-401
-
Constructing side chains on near-native main chains for ab initio protein structure prediction.
Samudrala R,
Huang ES, Koehl P, Levitt M.
Protein Eng.
2000;
13
(7):
453-7
-
Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches.
Samudrala R,
Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R.
Pac Symp Biocomput.
2000:
179-90
-
Expectations from structural genomics.
Brenner SE,
Levitt M.
Protein Sci.
2000;
9
(1):
197-200
-
De novo protein design. I. In search of stability and specificity.
Koehl P,
Levitt M.
J Mol Biol.
1999;
293
(5):
1161-81
-
De novo protein design. II. Plasticity in sequence space.
Koehl P,
Levitt M.
J Mol Biol.
1999;
293
(5):
1183-93
-
A brighter future for protein structure prediction.
Koehl P,
Levitt M.
Nat Struct Biol.
1999;
6
(2):
108-11
-
A combined approach for ab initio construction of low resolution protein tertiary structures from sequence.
Samudrala R,
Xia Y, Levitt M, Huang ES.
Pac Symp Biocomput.
1999:
505-16
-
Ab initio protein structure prediction using a combined hierarchical approach.
Samudrala R,
Xia Y, Huang E, Levitt M.
Proteins.
1999:
Suppl 3
194-8
-
Structure-based conformational preferences of amino acids.
Koehl P,
Levitt M.
Proc Natl Acad Sci U S A.
1999;
96
(22):
12524-9
-
The PRESAGE database for structural genomics.
Brenner SE,
Barken D, Levitt M.
Nucleic Acids Res.
1999;
27
(1):
251-3
-
A unified statistical framework for sequence comparison and structure comparison.
Levitt M,
Gerstein M.
Proc Natl Acad Sci U S A.
1998;
95
(11):
5913-20
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds.
Park BH,
Huang ES, Levitt M.
J Mol Biol.
1997;
266
(4):
831-46
-
Packing as a structural basis of protein stability: understanding mutant properties from wildtype structure.
Lee C,
Levitt M.
Pac Symp Biocomput.
1997:
245-55
-
Protein folding: the endgame.
Levitt M,
Gerstein M, Huang E, Subbiah S, Tsai J.
Annu Rev Biochem.
1997:
66
549-79
-
Competitive assessment of protein fold recognition and alignment accuracy.
Levitt M,
Proteins.
1997:
Suppl 1
92-104
-
Simulating the minimum core for hydrophobic collapse in globular proteins.
Tsai J,
Gerstein M, Levitt M.
Protein Sci.
1997;
6
(12):
2606-16
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys.
Park B,
Levitt M.
J Mol Biol.
1996;
258
(2):
367-92
-
From structure to sequence and back again.
Hinds DA,
Levitt M.
J Mol Biol.
1996;
258
(1):
201-9
-
Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations.
Huang ES,
Subbiah S, Tsai J, Levitt M.
J Mol Biol.
1996;
257
(3):
716-25
-
Through the breach.
Levitt M,
Curr Opin Struct Biol.
1996;
6
(2):
193-4
-
Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
Gerstein M,
Levitt M.
Proc Int Conf Intell Syst Mol Biol.
1996:
4
59-67
-
Recognizing native folds by the arrangement of hydrophobic and polar residues.
Huang ES,
Subbiah S, Levitt M.
J Mol Biol.
1995;
252
(5):
709-20
-
The complexity and accuracy of discrete state models of protein structure.
Park BH,
Levitt M.
J Mol Biol.
1995;
249
(2):
493-507
-
Exploring conformational space with a simple lattice model for protein structure.
Hinds DA,
Levitt M.
J Mol Biol.
1994;
243
(4):
668-82
-
Different protein sequences can give rise to highly similar folds through different stabilizing interactions.
Laurents DV,
Subbiah S, Levitt M.
Protein Sci.
1994;
3
(11):
1938-44
-
Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core.
Subbiah S,
Laurents DV, Levitt M.
Curr Biol.
1993;
3
(3):
141-8
-
Water: now you see it, now you don't.
Levitt M,
Park BH.
Structure.
1993;
1
(4):
223-6
-
Protein unfolding pathways explored through molecular dynamics simulations.
Daggett V,
Levitt M.
J Mol Biol.
1993;
232
(2):
600-19
-
Realistic simulations of native-protein dynamics in solution and beyond.
Daggett V,
Levitt M.
Annu Rev Biophys Biomol Struct.
1993:
22
353-80
-
Accurate modeling of protein conformation by automatic segment matching.
Levitt M,
J Mol Biol.
1992;
226
(2):
507-33
-
Molecular dynamics simulations of helix denaturation.
Daggett V,
Levitt M.
J Mol Biol.
1992;
223
(4):
1121-38
-
A lattice model for protein structure prediction at low resolution.
Hinds DA,
Levitt M.
Proc Natl Acad Sci U S A.
1992;
89
(7):
2536-40
-
A model of the molten globule state from molecular dynamics simulations.
Daggett V,
Levitt M.
Proc Natl Acad Sci U S A.
1992;
89
(11):
5142-6
-
Structural and kinetic studies of the Fab fragment of a monoclonal anti-spin label antibody by nuclear magnetic resonance.
Theriault TP,
Leahy DJ, Levitt M, McConnell HM, Rule GS.
J Mol Biol.
1991;
221
(1):
257-70
-
Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core.
Lee C,
Levitt M.
Nature.
1991;
352
(6334):
448-51
-
Real-time interactive frequency filtering of molecular dynamics trajectories.
Levitt M,
J Mol Biol.
1991;
220
(1):
1-4
-
Protein Folding
Levitt M,
Curr. Opinions Struct. Biol..
1991:
1
224-229
-
Accurate simulation of protein dynamics in solution.
Levitt M,
Sharon R.
Proc Natl Acad Sci U S A.
1988;
85
(20):
7557-61
-
Contribution of tryptophan residues to the combining site of a monoclonal anti dinitrophenyl spin-label antibody.
Anglister J,
Bond MW, Frey T, Leahy D, Levitt M, McConnell HM, Rule GS, Tomasello J, Whittaker M.
Biochemistry.
1987;
26
(19):
6058-64
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