Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM. "A genetically encoded photoactivatable
Leaver-Fay, A; Snoeyink, J; Kuhlman, B
"On-the-fly rotamer pair energy evaluation in protein design ".
Hu, XZ; Wang, HC; Ke, HM; Kuhlman, B
"Computer-Based
Redesign of a beta Sandwich Protein Suggests that Extensive Negative
Design Is Not Required for De Novo beta Sheet Design ".<\br>
STRUCTURE.
2008 Dec 10;16(12):1799-805.
Renfrew PD, Butterfoss GL, Kuhlman B.
"Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.".
Hu X, Wang H, Ke H, Kuhlman B.
"High-resolution design of a protein loop. ".
Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B.
"Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. ".
Eletr ZM, Kuhlman B. "Sequence Determinants of E2-E6AP Binding Affinity and
Specificity".
Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss
GL, Kuhlman B, Carter CW Jr. "A
minimal TrpRS catalytic domain supports sense/antisense
ancestry of class I and II aminoacyl-tRNA synthetases."
Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B."Maintaining solvent accessible surface area under rotamer substitution for protein design."
Ambroggio XI, Kuhlman B."Design
of protein conformational switches."
Hu X, Kuhlman B.
"Protein design simulations suggest that side-chain
conformational entropy is not a strong determinant of
amino acid environmental preferences."
Liu Y, Kuhlman B."RosettaDesign
server for protein design."
Ambroggio XI, Kuhlman B.
"Computational design of a single amino acid sequence
that can switch between two distinct protein folds. "
Jiang L, Kuhlman B,
Kortemme T, Baker D "A "solvated rotamer" approach to
modeling water-mediated hydrogen bonds at
protein-protein interfaces." Eletr ZM, Huang DT, Duda
DM, Schulman BA, Kuhlman B "E2 conjugating enzymes
must disengage from their E1 enzymes before E3-dependent
ubiquitin and ubiquitin-like transfer. "
Leaver-Fay A, Kuhlman B,
Snoeyink J. "An adaptive dynamic programming
algorithm for the side chain placement problem "
Butterfoss GL, Kuhlman B.
"Computer-Based Design of Novel Protein Structures."
Kuhlman B, Baker D.
"Exploring folding free energy landscapes using
computational protein design."
Science. 2003 Nov 21;302(5649):1364-8.PMID: 14631033 PMID: 14631033 [PubMed - indexed for MEDLINE] [view] Dantas G, Kuhlman B,
Callender D, Wong M, Baker D., "A large scale test of
computational protein design: folding and stability of
nine completely redesigned globular proteins." Tsai J, Bonneau R,
Morozov AV, Kuhlman B, Rohl CA, Baker D, "An improved
protein decoy set for testing energy functions for
protein structure prediction." Gray JJ, Moughon S, Wang
C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D.,
"Protein-protein docking with simultaneous optimization
of rigid-body displacement and side-chain
conformations." Nauli S, Kuhlman B, Le
Trong I, Stenkamp RE, Teller D, Baker D, "Crystal
structures and increased stabilization of the protein G
variants with switched folding pathways NuG1 and NuG2."
Kuhlman B, O'Neill JW,
Kim DE, Zhang KY, Baker D., "Accurate computer-based
design of a new backbone conformation in the second turn
of protein L." Kuhlman B, O'Neill JW,
Kim DE, Zhang KY, Baker D., "Conversion of monomeric
protein L to an obligate dimer by computational protein
design." Nauli S, Kuhlman B, Baker
D., "Computer-based redesign of a protein folding
pathway." Kuhlman B, Baker D.,
"Native protein sequences are close to optimal for their
structures." J Mol Biol. 1999 May 28;289(1):167-74.PMID: 10339414 [PubMed - indexed for MEDLINE] [view] Sato S, Kuhlman B, Wu WJ,
Raleigh DP., "Folding of the multidomain ribosomal
protein L9: the two domains fold independently with
remarkably different rates." Kuhlman B, Luisi DL,
Young P, Raleigh DP., "pKa values and the pH
dependent stability of the N-terminal domain of L9 as
probes of electrostatic interactions in the denatured
state. Differentiation between local and nonlocal
interactions." Kuhlman B, Luisi DL,
Evans PA, Raleigh DP., "Global analysis of the
effects of temperature and denaturant on the folding and
unfolding kinetics of the N-terminal domain of the
protein L9." Kuhlman B, Raleigh DP.,
"Global analysis of the thermal and chemical
denaturation of the N-terminal domain of the ribosomal
protein L9 in H2O and D2O. Determination of the
thermodynamic parameters, deltaH(o), deltaS(o), and
deltaC(o)p and evaluation of solvent isotope effects."
Vugmeyster L, Kuhlman B,
Raleigh DP., "Amide proton exchange measurements as a
probe of the stability and dynamics of the N-terminal
domain of the ribosomal protein L9: comparison with the
intact protein." Spector S, Kuhlman B,
Fairman R, Wong E, Boice JA, Raleigh DP.,
"Cooperative folding of a protein mini domain: the
peripheral subunit-binding domain of the pyruvate
dehydrogenase multienzyme complex." Kuhlman B, Boice JA,
Fairman R, Raleigh DP., "Structure and stability of
the N-terminal domain of the ribosomal protein L9:
evidence for rapid two-state folding." Kuhlman B, Yang HY, Boice
JA, Fairman R, Raleigh DP., "An exceptionally stable
helix from the ribosomal protein L9: implications for
protein folding and stability." Kuhlman B, Boice JA, Wu
WJ, Fairman R, Raleigh DP., "Calcium binding peptides
from alpha-lactalbumin: implications for protein folding
and stability." |
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