Publications
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The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning.
Kalisman N,
Schröder GF, Levitt M.
Structure.
2013;
21
(4):
540-9
-
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.
Brunger AT,
Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF.
Acta Crystallogr D Biol Crystallogr.
2012;
68
(Pt 4):
391-403
-
Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice.
Moreno-Hernández S,
Levitt M.
Proteins.
2012;
80
(6):
1683-93
-
Evaluating mixture models for building RNA knowledge-based potentials.
Sim AY,
Schwander O, Levitt M, Bernauer J.
J Bioinform Comput Biol.
2012;
10
(2):
1241010
-
Improving the accuracy of macromolecular structure refinement at 7 Å resolution.
Brunger AT,
Adams PD, Fromme P, Fromme R, Levitt M, Schröder GF.
Structure.
2012;
20
(6):
957-66
-
KoBaMIN: a knowledge-based minimization web server for protein structure refinement.
Rodrigues JP,
Levitt M, Chopra G.
Nucleic Acids Res.
2012;
40
(Web Server issue):
W323-8
-
Modeling and design by hierarchical natural moves.
Sim AY,
Levitt M, Minary P.
Proc Natl Acad Sci U S A.
2012;
109
(8):
2890-5
-
Modeling nucleic acids.
Sim AY,
Minary P, Levitt M.
Curr Opin Struct Biol.
2012;
22
(3):
273-8
-
Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images.
Zhang J,
Minary P, Levitt M.
Proc Natl Acad Sci U S A.
2012;
109
(25):
9845-50
-
Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling.
Kalisman N,
Adams CM, Levitt M.
Proc Natl Acad Sci U S A.
2012;
109
(8):
2884-9
-
Clustering to identify RNA conformations constrained by secondary structure.
Sim AY,
Levitt M.
Proc Natl Acad Sci U S A.
2011;
108
(9):
3590-5
-
Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Zhang J,
Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W.
Structure.
2011;
19
(5):
633-9
-
Normal modes of prion proteins: from native to infectious particle.
Samson AO,
Levitt M.
Biochemistry.
2011;
50
(12):
2243-8
-
Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes.
Bray JK,
Weiss DR, Levitt M.
Biophys J.
2011;
101
(12):
2966-9
-
Remarkable patterns of surface water ordering around polarized buckminsterfullerene.
Chopra G,
Levitt M.
Proc Natl Acad Sci U S A.
2011;
108
(35):
14455-60
-
Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm.
Minary P,
Levitt M.
J Comput Biol.
2010;
17
(8):
993-1010
-
Consistent refinement of submitted models at CASP using a knowledge-based potential.
Chopra G,
Kalisman N, Levitt M.
Proteins.
2010;
78
(12):
2668-78
-
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
-
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.
Saha M,
Levitt M, Chiu W.
Bioinformatics.
2010;
26
(12):
i301-9
-
Mechanism of folding chamber closure in a group II chaperonin.
Zhang J,
Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W.
Nature.
2010;
463
(7279):
379-83
-
Super-resolution biomolecular crystallography with low-resolution data.
Schröder GF,
Levitt M, Brunger AT.
Nature.
2010;
464
(7292):
1218-22
-
Can morphing methods predict intermediate structures?
Weiss DR,
Levitt M.
J Mol Biol.
2009;
385
(2):
665-74
-
Generalized ensemble methods for de novo structure prediction.
Shmygelska A,
Levitt M.
Proc Natl Acad Sci U S A.
2009;
106
(5):
1415-20
-
Nature of the protein universe.
Levitt M,
Proc Natl Acad Sci U S A.
2009;
106
(27):
11079-84
-
Outcome of a workshop on applications of protein models in biomedical research.
Schwede T,
Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA.
Structure.
2009;
17
(2):
151-9
-
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
-
How hydrophobic buckminsterfullerene affects surrounding water structure.
Weiss DR,
Raschke TM, Levitt M.
J Phys Chem B.
2008;
112
(10):
2981-90
-
Inhibition mechanism of the acetylcholine receptor by alpha-neurotoxins as revealed by normal-mode dynamics.
Samson AO,
Levitt M.
Biochemistry.
2008;
47
(13):
4065-70
-
Probing protein fold space with a simplified model.
Minary P,
Levitt M.
J Mol Biol.
2008;
375
(4):
920-33
-
Solvent dramatically affects protein structure refinement.
Chopra G,
Summa CM, Levitt M.
Proc Natl Acad Sci U S A.
2008;
105
(51):
20239-44
-
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
-
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
-
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
-
Spatial regulation and the rate of signal transduction activation.
Batada NN,
Shepp LA, Siegmund DO, Levitt M.
PLoS Comput Biol.
2006;
2
(5):
e44
-
An atomic environment potential for use in protein structure prediction.
Summa CM,
Levitt M, Degrado WF.
J Mol Biol.
2005;
352
(4):
986-1001
-
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
-
Describing RNA structure by libraries of clustered nucleotide doublets.
Sykes MT,
Levitt M.
J Mol Biol.
2005;
351
(1):
26-38
-
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
-
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
-
Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution.
Xia Y,
Levitt M.
Proteins.
2004;
55
(1):
107-14
-
Simulating protein evolution in sequence and structure space.
Xia Y,
Levitt M.
Curr Opin Struct Biol.
2004;
14
(2):
202-7
-
The ASTRAL Compendium in 2004.
Chandonia JM,
Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.
Nucleic Acids Res.
2004;
32
(Database issue):
D189-92
-
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
-
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
-
Protein decoy assembly using short fragments under geometric constraints.
Kolodny R,
Levitt M.
Biopolymers.
2003;
68
(3):
278-85
-
ASTRAL compendium enhancements.
Chandonia JM,
Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.
Nucleic Acids Res.
2002;
30
(1):
260-3
-
Design of an optimal Chebyshev-expanded discrimination function for globular proteins.
Fain B,
Xia Y, Levitt M.
Protein Sci.
2002;
11
(8):
2010-21
-
Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G.
Tsai J,
Levitt M.
Biophys Chem.
2002:
101-102
187-201
-
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
-
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
-
Sequence variations within protein families are linearly related to structural variations.
Koehl P,
Levitt M.
J Mol Biol.
2002;
323
(3):
551-62
-
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
-
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
-
A novel method for sampling alpha-helical protein backbones.
Fain B,
Levitt M.
J Mol Biol.
2001;
305
(2):
191-201
-
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
-
The birth of computational structural biology.
Levitt M,
Nat Struct Biol.
2001;
8
(5):
392-3
-
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
-
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
-
Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction.
Samudrala R,
Levitt M.
Protein Sci.
2000;
9
(7):
1399-401
-
Expectations from structural genomics.
Brenner SE,
Levitt M.
Protein Sci.
2000;
9
(1):
197-200
-
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
-
The ASTRAL compendium for protein structure and sequence analysis.
Brenner SE,
Koehl P, Levitt M.
Nucleic Acids Res.
2000;
28
(1):
254-6
-
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
-
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
-
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
-
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.
Tsai J,
Levitt M, Baker D.
J Mol Biol.
1999;
291
(1):
215-25
-
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
-
Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods.
Huang ES,
Koehl P, Levitt M, Pappu RV, Ponder JW.
Proteins.
1998;
33
(2):
204-17
-
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.
Gerstein M,
Levitt M.
Protein Sci.
1998;
7
(2):
445-56
-
Simulating water and the molecules of life.
Gerstein M,
Levitt M.
Sci Am.
1998;
279
(5):
100-5
-
A retrospective analysis of CASP2 threading predictions.
Marchler-Bauer A,
Levitt M, Bryant SH.
Proteins.
1997:
Suppl 1
83-91
-
A structural census of the current population of protein sequences.
Gerstein M,
Levitt M.
Proc Natl Acad Sci U S A.
1997;
94
(22):
11911-6
-
Competitive assessment of protein fold recognition and alignment accuracy.
Levitt M,
Proteins.
1997:
Suppl 1
92-104
-
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
-
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
-
Through the breach.
Levitt M,
Curr Opin Struct Biol.
1996;
6
(2):
193-4
-
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
-
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
-
Structural diversity in a conserved cholera toxin epitope involved in ganglioside binding.
Shoham M,
Scherf T, Anglister J, Levitt M, Merritt EA, Hol WG.
Protein Sci.
1995;
4
(5):
841-8
-
The complexity and accuracy of discrete state models of protein structure.
Park BH,
Levitt M.
J Mol Biol.
1995;
249
(2):
493-507
-
The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.
Gerstein M,
Tsai J, Levitt M.
J Mol Biol.
1995;
249
(5):
955-66
-
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
-
Exploring conformational space with a simple lattice model for protein structure.
Hinds DA,
Levitt M.
J Mol Biol.
1994;
243
(4):
668-82
-
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
-
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
-
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
-
Accurate modeling of protein conformation by automatic segment matching.
Levitt M,
J Mol Biol.
1992;
226
(2):
507-33
-
Induced peptide conformations in different antibody complexes: molecular modeling of the three-dimensional structure of peptide-antibody complexes using NMR-derived distance restraints.
Scherf T,
Hiller R, Naider F, Levitt M, Anglister J.
Biochemistry.
1992;
31
(30):
6884-97
-
Molecular dynamics simulations of helix denaturation.
Daggett V,
Levitt M.
J Mol Biol.
1992;
223
(4):
1121-38
-
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
-
Enhanced stability of subtilisin by three point mutations.
Narhi LO,
Stabinsky Y, Levitt M, Miller L, Sachdev R, Finley S, Park S, Kolvenbach C, Arakawa T, Zukowski M.
Biotechnol Appl Biochem.
1991;
13
(1):
12-24
-
Protein Folding
Levitt M,
Curr. Opinions Struct. Biol..
1991:
1
224-229
-
Real-time interactive frequency filtering of molecular dynamics trajectories.
Levitt M,
J Mol Biol.
1991;
220
(1):
1-4
-
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
-
NMR-derived model for a peptide-antibody complex.
Zilber B,
Scherf T, Levitt M, Anglister J.
Biochemistry.
1990;
29
(43):
10032-41
-
Conformations of immunoglobulin hypervariable regions.
Chothia C,
Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR.
Nature.
1989 Dec 21-28;
342
(6252):
877-83
-
A humanized antibody that binds to the interleukin 2 receptor.
Queen C,
Schneider WP, Selick HE, Payne PW, Landolfi NF, Duncan JF, Avdalovic NM, Levitt M, Junghans RP, Waldmann TA.
Proc Natl Acad Sci U S A.
1989;
86
(24):
10029-33
-
Probing antibody diversity by 2D NMR: comparison of amino acid sequences, predicted structures, and observed antibody-antigen interactions in complexes of two antipeptide antibodies.
Levy R,
Assulin O, Scherf T, Levitt M, Anglister J.
Biochemistry.
1989;
28
(18):
7168-75
-
Stabilization of phage T4 lysozyme by engineered disulfide bonds.
Matsumura M,
Becktel WJ, Levitt M, Matthews BW.
Proc Natl Acad Sci U S A.
1989;
86
(17):
6562-6
-
Accurate simulation of protein dynamics in solution.
Levitt M,
Sharon R.
Proc Natl Acad Sci U S A.
1988;
85
(20):
7557-61
-
Aromatic rings act as hydrogen bond acceptors.
Levitt M,
Perutz MF.
J Mol Biol.
1988;
201
(4):
751-4
-
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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