Publications
E-mail tec3@utah.edu for access to the local PDF links!
2023
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, N Forouzesh, TJ Giese, AW Gotz, H Gohlke, S Izadi, K Kasavajhala, MC Kaymak, E King, T Kurtzman, TS Lee, P Li, J Liu, T Luchko. R Luo, M Manathinga, MR Machado, HM Nguyen, KA O’Hearn, A Onufriev, F Pan, S Pantano, R Qi, A Rahnamoun, A Risheh, S Schott-Verdugo, A Shajan, J Swails, J Wang, H Wei, X Wu, S Zhang, S Zhao, Q Zu, TE Cheatham, III, DR Roe, A Roitberg, C Simmerling, DM York, MC Nagan and KM Merz, Jr. "AmberTools". J. Chem Info Modeling 63, 6183-6191 (2023) https://doi.org:10.1021/acs.jcim.3c01153
J Cutcher-Gershenfeld, T Middelkoop, D Brunson, T Cheatham, J Fosso Tande, D Jennewein, T Battelle, J Ma, LA Michael, H Neeman and P Schmitz. "Professionalization of Research Computing and Data: An Expanded Agenda" PEARC '23: Practice and Experience in Advanced Research Computing 129-136 (2023). Won Best Paper in the Workforce Development Track. https://doi.org/10.1145/3569951.3593610
O Love, R Galindo-Murillo, M Zgarbová, J Šponer, P Jurečka and TE Cheatham, III. "Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition." J. Chem. Theory Comput. 19, 4299-4307 (2023). https://doi.org:10.1021/acs.jctc.3c00233
L Winkler and TE Cheatham, III. "Benchmarking the Drude polarizable force field using the r(GACC) tetranucleotide." J. Chem. Info. Modeling 63, 2505-2511 (2023). https://doi.org:10.1021/acs.jcim.3c00250
L Winkler, R Galindo-Murillo and TE Cheatham, III. "The structures and dynamics of DNA mini-dumbbells are force field dependent". J. Chem. Theory Comp. 19, 2198-2212 (2023). https://doi.org:10.1021/acs.jctc.3c00130
T Rajasekaran, G Freestone, R Galindo-Murillo, B Lugato, H Gaus, M Migawa, E Swayze, TE Cheatham, III, P Seth and S Hanessian. "Systematic investigation of tether length and phosphorous configuration in backbone constrained macrocyclic nucleic acids to modulate binding kinetics for RNA". J. Organic Chem. 88, 3599-3614 (2023). https://doi.org:10.1021/acs.joc.2c02796
2022
T Hacker, P Smith, D Brunson, L Arafune, T Cheatham, and E Deelman. "Building the research innovation workforce: Challenges and recommendations from a virtual workshop to advance the research computing community." In Practice and Experience in Advanced Research Computing (PEARC '22), July 10–14, 2022, Boston, MA, USA. ACM, New York, NY, USA 7 Pages. https://doi.org/10.1145/3491418.3530288
R Galindo*, L Winkler*, J Ma, F Hanelli, A Fleming, C Burrows, and T Cheatham, "Riboflavin Stabilizes Abasic, Oxidized G-Quadruplex Structures". Biochemistry 61, 265-275 (2022). https://doi.org/10.1021/acs.biochem.1c00598
T Rajasekaran, GC Freestone, R Galindo-Murillo, B Lugato, L Rico, JC Salinas, H Gaus, MT Migawa, EE Swayze, TE Cheatham, III, S Hanessian, and PP Seth, "Backbone hydrocarbon-constrained nucleic acids modulate hybridization kinetics for RNA". J. Amer. Chem. Soc. 144, 1941-1950 (2022). https://doi.org/10.1021/jacs.1c12323
2021
G da Rosa, L Grille, V Calzada, K Ahmad, JP Arcon, F Battistini, G
Bayarri, T Bishop, P Carloni, T Cheatham III, R Collepardo-Guevara,
J Czub, JR Espinosa, R Gallino-Murillo, SA Harris, A Hospital, C
Laughton, JH Maddocks, A Noy, M Orozco, M Pasi, A Perez, D
Petkeviciute-Gerlach, R Sharma, R Sun, and PD
Dans. "Sequence-dependent structural properties of B-DNA: what have
we learned in 40 years?" Biophysical Reviews 13, 995-1005
(2021).
[
local PDF:
Biophys Rev link
]
JL Kessler, G Kang, Z Qin, H Kang, FG Whitby, TE Cheatham III, CP
Hill, Y Li, and SM Yu, "Peptiod Residues Make Diverse, Hyperstable
Collagen Triple-Helices". J. Amer. Chem. Soc. 143, 29,
10910-10919 (2021)
[
local PDF:
JACS link
]
P Schmitz, S Yockell, C Mizumoto, T Cheatham III, and Dana
Brunson, "Advancing the Workforce that Supports Computationally and
Data Intensive Research". Computing in Sci. & Eng.
Sept.-Oct. pp.19-27, vol 23
(2021). https://doi.org/10.1109/MCSE.2021.3098421
[
Journal link]
R Galindo-Murillo and TE Cheatham, "Ethidium bromide interactions with
DNA: an exploration of a classic DNA-ligand complex with unbiased
molecular dynamics simulations." Nucleic Acids
Res. 49, 3735-3747. https://doi.org/10.1093/nar/gkab143
[
local PDF:
NAR link:
See
the cool movie!
]
J Ma, T Battelle, K Bulekova, A Culich, J Goodhue, J Pessin, V Sochat,
D Brunson, T Cheatham, S Najafi, C Hill, A Del Maestro, B Segee, R
Zottola, S Valcourt, Z Braiterman, R Singh, R Thoelen, and J Smith.
"Ask.Cyberinfrastructure.org: Creating a Platform for Self-Service
Learning and Collaboration in the Rapidly Changing Environment of
Research Computing" J. Comp. Sci. Education (2021).
DOI: https://doi.org/10.22369/issn.2153-4136/12/2/9
[
local PDF:
JCSE link
]
2020
S Broude Geva, D Brunson, T Cheatham III, J Deaton, J Griffioen,
CW Hillegas, DM Jennewein, G Krovitz, T Magle, P Schmitz, K Tomko, and
JC Wilgenbusch. "Fostering Collaboration Among Organizations in the
Research Computing and Data Ecosystem". In Practice and Experience in
Advanced Research Computing (PEARC ’20), July 26–30, 2020, Portland,
OR, USA. ACM, New York, NY, USA, 13 pages (2020).
https://doi.org/10.1145/3311790.3396645
P Schmitz, C Mizumoto, J Hicks, D Brunson, G Krovitz, JR Bottum,
J Cutcher-Gershenfeld, K Wetzel, and T Cheatham III. "A Research
Computing and Data Capabilities Model for Strategic
Decision-Making". In Practice and Experience in Advanced Research
Computing (PEARC ’20), July 26–30, 2020, Portland, OR, USA. ACM, New
York, NY, USA, 12 pages (2020). https://doi.org/10.1145/3311790.3396643
R Galindo-Murillo, L Winkler, JC Garcia-Ramos, L Ruiz-Azuara, F
Cortez-Guzman, and TE Cheatham III. "Ancillary Ligand in Ternary CuII
Complexes Guides Binding Selectivity Toward Minor-Groove DNA."
J. Phys. Chem. B 124, 11648-11658
(2020). https://doi.org/10.1021/acs.jpcb.0c09296
R Galindo-Murillo, TE Cheatham III, and RC Hopkins. "Exploring
potentially alternative non-canonical DNA duplex structures through
simulation." J. Biomol. Struct. Dyn. 37, 2201-2210 (2019) doi:
10.1080/07391102.2018.1483839
J Ma, A Culich, T Battelle, D Brunson, T Cheatham, J Goodhue, C Hill,
L Passin, J Smith, and S Yockel.
"On launching Ask.CI, a Q & A platform for research computing using
StaackExchange and Discouse" In SC18 Proceedings (2018).
DOI: https://doi.org/10.22369/issn.2153-4136/12/2/9
AJ Monaghan, B Milash, T Magle, T Hauser, TE Cheatham, PJ Burns,
S Knuth, AM Orendt, S White, D Paschal, HJ Siegel, T Kaiser, AM
Johnson, and B Yeager. "Improving regional cyberinfrastructure
services through collaboration: Cyberteam for the Rocky Mountain
Advanced Computing Consortium." In Practice and Experience in Advanced
Research Computing (PEARC’ 19), July 28-August 1, 2019, Chicago, IL,
USA. ACM, New York, NY, USA, 8
pages. https://doi.org/10.1145/3332186.3332232.
CA Stewart, DY Hancock, J Wernert, T Furlani, D Lifka, A Sill, N
Berente, DF McMullen, T Cheatham, A Apon, R Payne, and SD
Slavin. "Assessment of non-financial returns cyberinfrastructure: A survey of current methods." In
JARC '19 Proceedings of the Humans in the Loop: Enabling and Facilitating
Research on Cloud Computing, July 2019, 2, 1-10 (2019).
pages. https://doi.org/10.1145/3355738.3355749.
CA Stewart, DY Hancock, J Wernert, T Furlani, D Lifka, A Sill, N
Berente, DF McMullen, T Cheatham, A Apon, R Payne, and SD
Slavin. "Assessment of financial returns on investments in
cyberinfrastructure facilities: A survey of current methods." In
Practice and Experience in Advanced Research Computing (PEARC ’19),
July 28-August 1, 2019, Chicago, IL, USA. ACM, New York, NY, USA, 8
pages. https://doi.org/10.1145/3332186.3332228.
R Galindo-Murillo and TE Cheatham, III. "Lessons learned in
atomistic simulation of double-stranded DNA: Solvation and salt
concerns." Living J. Comp. Mol. Sci.
https://doi.org/10.33011/livecoms.1.2.9974 (2019).
G Fox, O Beckstein, J Qui, D Crandall, G von Laszewski, J Paden, S Jha, F Wang, M
Marathe, A Vullikanti, and T Cheatham. "Contributions to
High-Performance Big Data Computing" In Future Trends
of HPC in a Disruptive Scenario IOS Press, Volume 34 of Advances
in Parallel Computing (2019).
DR Roe and TE Cheatham, III. "Parallelization of CPPTRAJ enables
large scale analysis of molecular dynamics trajectory data."
J. Comp. Chem. 39, 2110-2117 (2018). DOI:10.1002/jcc.25382.
HS Hayatshahi, NM Henriksen and TE Cheatham III. "Consensus
Conformations of Dinucleoside Monophosphates Described with
Well-Converged Molecular Dynamics Simulations."
J. Chem. Theory Comput. 14:1456-1470 (2018).
DOI: 10.1021/acs.jctc.7b00581.
SP Cornillie, BJ Bruno, CS Lim and TE Cheatham, III.
"Computational Modeling of Stapled Peptides toward a Treatment Strategy
for CML and Broader Implications in the Design of Lengthy Peptide
Therapeutics."
J. Phys. Chem. B. 122:3864-3875 (2018).
DOI:10.1021/acs.jpcb.8b01014.
IM Chrisman, MD Nemetchek, IMS Mitchell de Vera, J Shang, Z Heidari,
Y Long, H Reyes-Caballero, R Galindo-Murillo, TE Cheatham, III, AL Blayo, Y
Shin, J Fuhrmann, PR Griffin, TM Kamenecka, DJ Kojetin, and TS Hughes.
"Defining a conformational ensemble that directs activation of PPARγ."
Nature Comm. 9, 1794 (2018). DOI: 10.1038/s41467-018-04176-x.
I Paraskevakos, A Luckow, M Khoshlessan, G Chantzialexiou, TE
Cheatham, III, O Beckstein, GC Fox, and S. Jha. "Task-parallel
analysis of molecular dynamics trajectories." ICPP 2018 Proceedings of
the 47th International Conference on Parallel Processing, Eugene OR,
August 13-16 (2018) Article 49. DOI:10.1145/3225058.3225128
HS Hayatshahi, C Bergonzo, and TE Cheatham III. "Investigating the ion
dependence of the first unfolding step of GTPase-associating center
ribosomal RNA." J. Biomol. Struct. Dyn. 1-11
(2017). DOI:10.1080/07391102.2016.1274272.
HS Hayatshahi, DR Roe, R Galindo-Murillo, KB Hall, and TE
Cheatham, III. "Computational Assessment of Potassium and Magnesium
Ion Binding to a Buried Pocket in the GTPase-Associating Center
RNA." J. Phys. Chem. B 121, 451-462 (2017).
M Zgarbova, P Jurecka, F Lankas, Filip; TE Cheatham, III, J
Sponer, M Otyepka. "Influence of BII Backbone Substates on DNA
Twist: A Unified View and Comparison of Simulation and Experiment
for all 136 Distinct Tetranucleotide Sequences."
J. Chem. Info. Model. 57, 275-287 (2017).
Y Wang, BJ Bruno, S Cornillie, JM Nogieira, D Chen, TE
Cheatham, III, CS Lim, and D Chou. "Application of
thiol-yne/thiol-ene reactions for peptide and protein
macrocyclizations." Chemistry 23: 7087-7092 (2017).
C Bergonzo and TE Cheatham, III. "Mg2+ binding promotes SLV as
a scaffold in Varkud Satellite Ribozyme SLI-SLV kissing loop
junction." Biophys. J. 113, 313-320 (2017).
DOI:10.1016/j.bpj.2017.06.008.
R Galindo-Murillo and TE Cheatham III. "Computational DNA binding
studies of (-)-epigallocatechin-3-gallate." J. Biomol. Struct. Dyn. 3, 1-13
(2017). DOI:10.1080/07391102.2017.1389306.
M Xu, R Galindo-Murillo, TE Cheatham III, and RM Franzini.
"Dissociative reactions of benzonorbornadienes with tetrazines:
scope of leaving groups and mechanistic insights."
Org. Biomol. Chem. 15, 9855-9865 (2017). DOI:10.1039/c7ob02191g.
C Bergonzo, KB Hall, and TE Cheatham, III. "Divalent Ion
Dependent Conformational Changes in an RNA Stem-Loop Observed by
Molecular Dynamics." J. Chem. Theory Comp. 12, 3382–3389 (2016).
Y Hao, E Pierce, D Roe, M Morita, JA McIntosh, V Agarwal, TE
Cheatham III, EW Schmidt, and SK Nair. "Molecular basis of
broad-substrate selectivity of a peptide prenyltransferase." PNAS
113, 14037-14042 (2016).
Z Heidari, DR Roe, R Galindo-Murillo, JB Ghasemi, and TE Cheatham
III. "Using Wavelet Analysis To Assist in Identification of
Significant Events in Molecular Dynamics Simulations."
J. Chem. Inf. Model. 56, 1282-1291 (2016).
R Galindo-Murillo, JC Robertson, M Zgarbova, J Sponer, M Otyepka,
P Jurecka, and TE Cheatham III. "Assessing the current state of Amber
force field modifications for DNA." J. Chem. Theory Comp. 12,
4114-4127 (2016). DOI: 10.1021/acs.jctc.6b00186
JT Waters, X-J Lu, R Galindo-Murillo, JC Gumbart, HD Kim, TE Cheatham,
III and SC Harvey. "Transitions of double-stranded DNA between the A-
and B- forms."
J. Phys Chem. B 120, 8449-8456 (2016)
R Galindo-Murillo, DR Davis and TE Cheatham, III.
"Probing the influence of hypermodified residues within the tRNA3Lys
anticodon stem loop interacting with the A-loop primer sequence from
HIV-1." Biochemica Biophys. Acta 1860, 607-617 (2016).
M Zgarbova, J Sponer, M Otyepka, TE Cheatham, III, R
Galindo-Murillo, and P Jurecka. "Refinement of the sugar-phosphate
backbone torsion beta for the AMBER force fields improves the
description of Z-DNA and B-DNA."
J. Chem. Theory Comp. 11, 5723-5736 (2015).
JC Robertson and TE Cheatham, III. "DNA backbone BI/BII distribution
and dynamics in E2 protein-bound environment determined by molecular
dynamics simulation." J. Phys. Chem. B 119, 14111-14119 (2015).
R Galindo-Murillo and TE Cheatham, III. "Using information
about DNA structure and dynamics from experiment and simulation to
give insight into genome-wide association studies." Chapter 4 in
Translation Cardiometabolic Genomic Medicine, edited by A
Rodriguez-Oquendo, p 81-98 (2015).
JC Thibault, DR Roe, K Eilbeck, TE Cheatham, III, and JC
Facelli. "Development of an informatics infrastructure for data
exchange of biomolecular simulations: Architecture, data models, and
ontology." SAR and QSAR in Environmental Research (2015).
C Bergonzo, KB Hall, and TE Cheatham, III. "Stem-loop V of
Varkud satellite RNA exhibits characteristics of the Mg2+ bound
structure in the presence of monovalent
ions." J. Phys. Chem. B 119, 12355-12364 (2015).
C Bergonzo and TE Cheatham, III
"Improved force field parameters lead to a better description of RNA structure"
J. Chem. Theory Comp. 11, 3969-3972 [doi:10.1261/acs.jctc.5b00444] (2015).
AC Simmonett, FC Pickard IV, Y Shao, TE Cheatham, III and BR
Brooks "Efficient treatment of induced
diploles". J. Chem. Phys. 143, 074115 (2015).
C Bergonzo, NM Henriksen, DR Roe, and TE Cheatham, III
"Highly sampled tetranucleotide and tetraloop motifs enable evaluation
of common RNA force fields." RNA 29: 1578-1590 [doi:10.1261/rna.051102.115] (2015).
R Galindo-Murillo, JC Garcia-Ramos, L Ruiz-Azuara, TE Cheatham, III,
and F Cortes-Guzman. "Intercalation processes of copper complexes in
DNA." Nuc. Acids Res. 43: 5364-5376 (2015).
TE Cheatham, III and DR Roe. "The impact of heterogeneous
computing on workflows for biomolecular simulation and analysis."
Computing in Science and Engineering 17:2, 30-39 (2015).
R Galindo-Murillo, DR Roe, and TE Cheatham, III. "Convergence and
reproducibility in molecular dynamics simulations of the DNA duplex
d(GCACGAACGAACGAACGC)." Biochimica Biophys. Acta 1850, 1041-1058 (2015). doi: 10.1016/j.bbagen.2014.09.007.
M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, TE
Cheatham, III, PD Dans, B Jayaram, F Lankas, C Laughton, J Mitchell, R
Osman, M Orozco, A Perez, D Petkeviciute, N Spackova, J Sponer, K
Zakrzewska, and R Lavery. "μABC: A systematic microsecond molecular
dynamics study of tetranucleotide sequence effects in
B-DNA." Nuc. Acids Res. 42, 12272-12283 (2014).
R Galindo-Murillo, DR Roe, and TE Cheatham, III. "On the absence of
intrahelical DNA dynamics on the μs to ms timescale."
Nature Commun. 5:5152 (2014) doi: 10.1038/ncomms6152.
Z Lin, M Koch, M Abdel Aziz, D Tianero, R Galindo, TE Cheatham,
III, L Barrows, C Reilly, and E Schmidt. "Oxazinin A, A Pseudodimeric
Natural Product of Mixed Bio-synthetic Origin from a Filamentous
Fungus." Organic Letters 16, 4774-4777 (2014) doi: 10.1021/ol502227x.
P Stadlbauer, L Trantírek, TE Cheatham, J Koèa and J Sponer.
"Triplex intermediates in folding of human telomeric quadruplexes
probed by microsecond-scale molecular dynamics simulations."
Biochimie 105, 22-35 (2014) doi:10.1016/j.biochi.2014.07.009.
A Okal, S Cornillie, SJ Matissek, KJ Matissek, TE Cheatham, III
and CS Lim. "A re-engineered p53 chimera with enhanced
homo-oligomerization that maintains tumor suppressor
activity." Mol. Pharm. 11(7), 2442-2452 (2014).
NM Henriksen, H Hayatshahi, DR Davis, and TE Cheatham,
III. "Structural and energetic analysis of 2-aminobenzimidazole
inhibitors in complex with the hepatitis C virus IRES RNA using
molecular dynamics simulations." J. Chem. Info Model. 54(6), 1758-1772
(2014).
J Thibault, TE Cheatham, III, and JC Facelli. "iBIOMES Lite:
Summarizing biomolecular simulation data in limited settings."
J. Chem. Info Model. 54(6), 1810-1819 (2014).
R Galindo-Murillo and T.E. Cheatham, III. "DNA-binding dynamics and
energetics of Co, Ni, and Cu metallopeptides"
Chem. Med. Chem. 9(6), 1252-1259 (2014).
DR Roe, C Bergonzo, and T.E. Cheatham, III. "Evaluation of enhanced
sampling provided by accelerated molecular dynamics with Hamiltonian
replica exchange methods." J. Phys. Chem. B 118, 3543-3552 (2014).
JC Thibault, DR Roe, JC Facelii and T.E. Cheatham, III. "Data
model, dictionaries, and desiderata for biomolecular simulation data
indexing and sharing." J. Cheminformatics 6 (2014) doi:10.1186/1758-2946-6-4.
R Galindo-Murillo, C Bergonzo and T.E. Cheatham, III. "Molecular
modeling of nucleic acid structure: Setup and analysis."
Cur. Protocols Nucleic Acid Chemistry 56: 7.10.1-7.10.12 (2014).
C Bergonzo, N Henriksen, D Roe, J Swails, AE Roitberg,
and T.E. Cheatham, III. "Multi-dimensional replica exchange
molecular dynamics yields a converged ensemble of an RNA
tetranucleotide." J. Chem. Theory Comp. 10, 492-499 (2014).
N Ashton, DR Roe, R Weiss, TE Cheatham III and R. Stewart.
"Self-tensioning aquatic caddisfly silk: Ca2+-dependent
structure, strength, and load cycle hysteresis."
Biomacromolecules 14, 3668-3681 (2013).
R Galindo-Murillo, C Bergonzo and TE Cheatham, III.
"Molecular modeling of nucleic acid structure."
Current Protocols Nucleic Acid Chemistry 54: 7.5.1-7.5.13 (2013).
C Bergonzo, R Galindo-Murillo, and TE Cheatham, III.
"Molecular modeling of nucleic acid structure: Energy and
Sampling."
Current Protocols Nucleic Acid Chemistry 54: 7.8.1-7.8.21 (2013).
C Bergonzo, R Galindo-Murillo and TE Cheatham, III.
"Molecular modeling of nucleic acid structure: Electrostatics and
solvation"
Current Protocols Nucleic Acid Chemistry 55: 7.9.1-7.9.27 (2013).
TE Cheatham, III and D.A. Case. "Twenty-five years of nucleic
acid simulations."Biopolymers [in press] (2013).
D Roe and TE Cheatham, III. "PTRAJ and CPPTRAJ: Software for
processing and analysis of molecular dynamics trajectory
data." J. Chem. Theory Comp. 9, 3084-3095(2013).
...the long awaited PTRAJ paper!
J Sponer, A Mladek, N Spackova, X Cang, TE Cheatham, III
and S. Grimme. "Relative stability of different DNA guanine
quadruplex stem topologies derived using large-scale quantum-chemical
computations." J. Amer. Chem. Soc. 135, 9785-9796 (2013).
M Zgarbova, F Javier Luque, J Sponer, TE Cheatham, III,
M Otyepka, and P Jurecka. "Toward improved description of DNA
backbone: Revisiting epsilon and zeta torsion force field
parameters." J. Chem. Theory Comp. 9, 2339-2354 (2013).
P Stadlbauer, M Krepl, TE Cheatham, III, J Koca and
J. Sponer. "Structural dynamics of possible late-stage intermediates
in folding quadruplex DNA studied by molecular simulations."
Nuc. Acids Res. 41, 7128-7143 (2013).
NM Henriksen, DR Roe, and TE Cheatham, III. "Reliable oligonucleotide
conformational ensemble generation in explicit solvent for force field
assessment using reservoir replica exchange molecular dynamics simulations."
J. Phys. Chem. B 117m 491404927 (2013).
JC Thibault, JC Facelli, and TE Cheatham, III. "iBIOMES: Managing and
sharing biomolecular simulation data in a distributed environment."
J. Chem. Info. Model. 53, 726-736 (2013).
NM Henriksen, DR Davis, and TE Cheatham, III. "Molecular dynamics
re-refinement of two different small RNA loop structures using the
original NMR data suggest a common structure." J. Biomol. NMR
53, 321-339 (2012).
M Krepl, M Zgarbova, P. Stadlbauer, M Otyepka, P Banas, J Koca, TE
Cheatham, IIII, P Jurecka, and J Sponer. "Reference simulations of
noncanonical nucleic acids with different chi variants of the AMBER
force field: Quadruplex DNA, quadruplex RNA, and Z-DNA."
J. Chem. Theory Comp. 8, 2506-2520 (2012).
J Sponer, X Cang, and TE Cheatham, III. "Molecular dynamics
simulations of G-DNA and perspectives on the simulation of nucleic
acid structures." Methods 57(1): 25-39 (2012).
DL Beveridge, TE Cheatham, III, and M Mezei. "The ABCs of molecular
dynamics simulations on B-DNA, circa 2012." J. Bioscience
37, 379-397 (2012).
K Shahrokh, TE Cheatham, III, and GS Yost. "Conformational
dynamics of CYP3A4 demonstrate the important role of Arg212 coupled
with the opening of ingress, egress and solvent channels to
dehydrogenation of 4-hydroxy-tamoxifen."
Biochem. Biophys. Acta. 1820, 1605-1617 (2012) [ASAP].
Z. Lin, M. Flores, I. Forteza, N.M. Henriksen, G.P. Concepcion,
G. Rosenberg, M.G. Haygood, B.M. Olivera, A.R. Light, T.E. Cheatham,
III and E.W. Schmidt. "Totopotensamides, Polyketide-Cyclic Peptide
Hybrids from a Mollusk-Associated Bacterium Streptomyces sp."
J. Nat. Prod. 75, 644-649 (2012).
A.S. Dixon, G.D. Miller, B.J. Bruno, J.E. Constance, D.W. Woessner,
T.P. Fidler, J.C. Robertson, T.E. Cheatham, III and C.S. Lim.
"Improved coiled-coil design enhances interaction with Bcr-Abl and
induces apoptosis."
Mol. Pharm. 9, 187-195 (2012)
K. Shahrokh, A. Orendt, G. S. Yost, and T. E. Cheatham, III. "Quantum mechanically
derived AMBER-compatible heme parameters for various states of the
cytochrome P450 catalytic cycle."
J. Comp. Chem. 33, 119-133 (2012).
X. Cang, J. Sponer, and T. E. Cheatham, III
"Insight into G-DNA structural polymorphism and folding from sequence
and loop connectivity through free energy analysis."
J. Amer. Chem. Soc. 133, 14270-14279 (2011).
A. S. Dixon, S. S. Pendley, B. J. Bruno, D. W. Woessner, A. A. Shimpi,
T. E. Cheatham, III, and C. S. Lim. "Disruption of BCR-ABL coiled-coil
oligomerization by design." J. Biol. Chem. B 286. 27751-27760 (2011).
M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham,
III, and P. Jurecka. "Refinement of the Cornell et al. nucleic acid
force field based on reference quantum chemical calculations of
torsion profiles of the glycosidic torsion." J. Chem. Theory
Comp. 7, 2886-2902 (2011).
X. Wei, H. M. Henriksen, J. J. Skalicky, M. K. Harper, T.E. Cheatham,
III, C. M. Ireland, and R. M. Van Wagoner. "Araiosamines A-D:
Tris-bromoindole cyclic guanidine alkaloids from the marine sponge
clathria (Thalysias) araiosa."
J. Org. Chem. B 76, 5515-5523 (2011).
K. C. Thomas, M. Ethirajan, K. Shakrokh, H. Sun, J. Lee,
T.E. Cheatham, III, G. S. Yost, and C. A. Reilly. "Structure-activity
relationships of capsaicin analogs and transient receptor potential
vanilloid 1-mediated human lung epithelia cell toxicity."
J. Pharmacol. Exp. Ther. 337, 400-410 (2011).
X. Cang, J. Sponer, and T. E. Cheatham, III. "Explaining the varied
glycosidic conformational, G-tract length and sequence preferences for
anti-parallel G-quadruplexes." Nuc. Acids Res. 39, 4499-4512
(2011).
R. DeMille, T. E. Cheatham, III, and V. Molinero. "A coarse-grained
model of DNA with explicit solvation by water and ions."
J. Phys. Chem. B 115, 132-142 (2011). PMC-3019136
R. Lavery, K. Zakrzewska, D.L. Beveridge, T.C. Bishop, D.A. Case,
T.E. Cheatham, III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton,
J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh,
N. Spackova, and J. Sponer. "A systematic molecular dynamics study of
nearest-neighbor effects on base pair and base pair step conformations
and fluctuations in B-DNA." Nuc. Acids Res. 38, 299-313
(2010). PMCID: 2800215
T. Truong, H. Freedman, L. Le, T.E. Cheatham, III, J. Tuszynski,
and L. Huynh. "Explicitly-solvated ligand contribution to continuum
solvation models for binding free energies: Selectivity of
theophylline binding to an RNA aptamer." J. Phys. Chem. B 114, 2227-2237 (2010).
R. B. Paulsen, P. P. Seth, E. E. Swayze, R. H. Griffey,
J. J. Skalicky, T. E. Cheatham, III, and D. R. Davis. "Inhibitor
induced structure change in the HCV IRES domain IIa RNA."
Proc. Natl. Acad. Sci. 107, 7263-7268 (2010).
C. D. Moore, K. Shahrokh, S. F. Sontum, T. E. Cheatham, III, and G. S. Yost.
"Improved Cyp3A4 molecular models accurately predict Phe215
requirement for raloxifene dehydrogentation selectivity."
Biochemistry 49, 9011-9019 (2010).
P. Banas, D. Hollas, M. Zgarbova, P. Jurecka, M. Orozco, T. E. Cheatham,
III, J. Sponer, and M. Otyepka. "Performance of molecular mechanics
force fields for RNA simulations. Stability of UUCG and GNRA
hairpins." J. Chem. Theory Comp. 6, 3836-3849 (2010).
K.F. Wong, J.L. Sonnerberg, F. Paesani, T. Yamamoto, J. Vanicek, J. Zhang,
H.B. Schlegl, D.A. Case, T.E. Cheatham, III, W.H. Miller, and G.A. Voth.
"Proton transfer studied using a combined ab initio reactive potential
energy surface with quantum path integral methodology."
J. Chem. Theory Comp. 6, 2566-2580 (2010).
S. S. Pendley, Y. B. Yu, and T.E. Cheatham, III. "Molecular
dynamics guided study of salt bridge length dependence in both
fluorinated and non-fluorinated parallel dimeric coiled-coil
proteins." Proteins 74, 612-629 (2009) [DOI:
10.1002/prot.22177] PMCID: 2692595.
H. Wang, T.E. Cheatham, III, P.M. Gannett, and J. Lewis.
"Differential electronic states observed during the A-B DNA duplex
conformational transitions." Soft Matter 5, 685-690 (2009).
T. S. Han, M.-M. Zhang, A. Walewska, P. Gruszczynski,
C.R. Robertson, T.E. Cheatham, III, D. Yoshikami, B. M. Olivera, and
G. Bulaj. "Structurally-minimized-conotoxin analogs as sodium
channel blockers: Implications for designing conopeptide-based
therapeutics." Chem. Med. Chem. 4, 406-414 (2009).
In Suk Joung, O. Persil Cetinkol, N. V. Hud, and T.E. Cheatham, III. "Molecular
dynamics simulations and coupled nucleotide substitution experiments
indicate the nature of A-A base pairing and a putative structure of
the coralyne-induced homo-adenine duplex." Nuc. Acids Res. 37,
7715-7727 (2009). PMCID: 2794157
In Suk Joung, and T.E. Cheatham, III. "Molecular dynamics
simulations of the dynamic and energetic properties of alkali and
halide ions using water-model specific ion parameters."
J. Phys. Chem. B 113, 13279-13290 (2009). PMCID: 2755304
E. Fadrna, N. Spackova, J. Sarzynska, J. Koca, M. Orozco,
T.E. Cheatham, III, T. Kulinski, J. Sponer. "Single stranded loops of
quadruplex DNA as key benchmark for testing nucleic acids force
field." J. Chem. Theory Comp. 5, 2514-2530 (2009).
In Suk Joung, and T.E. Cheatham, III. "Determination of alkali
and halide monovalent ion parameters for use in explicitly solvated
biomolecular simulations." J. Phys. Chem. B 112, 9020-9041 (2008).
D. Svozil, J.E. Sponer, I. Marchan, A. Perez, T.E. Cheatham, III,
J. Luque, M. Orozco, and J. Sponer. "Geometrical and electronic
structure variability of the sugar-phosphate backbone in nucleic
acids." J. Phys. Chem. B 112, 8188-8197 (2008).
A. Perez, I. Marchan, D. Svozil, J. Sponer, T.E. Cheatham, III,
C.A. Laughton, M. Orozco. "Refinement of the AMBER force field for
nucleic acids. Improving the description of alpha/gamma conformers."
Biophys. J. 92, 3817-3829 (2007).
A. Wierzbicki, P. Dalal, T.E. Cheatham, III, J.E. Knickelbein,
A.D.J. Haymet, and J.D. Madura. "Antifreeze proteins at the ice/water
interface: Three calculated discriminating properties for orientation
of type I proteins." Biophys. J. 93, 1442-1451 (2007).
J. Shao, S. W. Tanner, N. Thompson, T.E. Cheatham, III. "Clustering
molecular dynamics trajectories: I. Characterizing the performance of
different clustering algorithms." J. Chem. Theory Comp. 3,
2312-2334 (2007).
P. Auffinger, T.E. Cheatham, III, and A. C. Vaiana. "Spontaneous
formation of KCl aggregates in biomolecular simulations: a force field
issue?." J. Chem. Theory Comp. 3, 1851-1859 (2007).
T.E. Cheatham, III and D.A. Case. "Using AMBER to simulate DNA and
DNA" in Computational Studies of DNA and RNA (Wiley) Editors,
J. Sponer and F. Lankas p. 45-72.
N. Spackova, T.E. Cheatham, III and J. Sponer. "Molecular dynamics
simulations of nucleic acids" in Computational Studies of DNA and RNA (Wiley) Editors,
J. Sponer and F. Lankas p. 301-326.
F. Paesani, W. Zhang, D.A. Case, T.E. Cheatham, III and G.A. Voth. "An
accurate and simple quantum model for liquid water."
J. Chem. Phys. 125, 184507 (2006).
T.N. Truong, M. Nayak,H. Huynh, T. Cook, P. Marajan, L.T. Tran,
J. Bharath, S. Jain, H.B. Pham, N. Nguyen, Y. Kim, S. Choe,
T.E. Cheatham, III, and J. Facelli, "Computational Science and
Engineering Online (CSE-Online): A cyberinfrastructure for scientific computing."
J. Chem. Info. Mod. 46, 971-984 (2006).
T. E. Cheatham, III "Molecular modeling and atomistic simulation of
nucleic acids."
Ann. Reports Comp. Chem. Editor: D. Spellmeyer, Vol 1, pp. 75-89.
D. A. Case, T.E. Cheatham, III, T.A. Darden, H. Gohlke, R. Luo,
K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and
R. Woods. "The AMBER biomolecular simulation programs."
J. Comp. Chem. 26, 1668-1688
S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham III,
E. Giudice, F. Lankas, R. Lavery, J. Maddocks, R. Osman, H. Sklenar,
K.M. Thayer, and P. Varnai. "Molecular dynamics simulations of the 136
unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence
context effects on the dynamical structures of the 10 unique
dinucleotide steps." Biophys. J. 89, 3721-3740.
D. L. Beveridge, G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham,
III, S. B. Dixit, E. Guidice, F. Lankas, R. Lavery, J. Maddocks,
R. Osman, H. Sklenar, G. Stoll, K. M. Thayer, P. Varnai, and
M. A. Young, "Molecular dynamics simulations of the 136 unique
tetranucleotide sequences of DNA oligonucleotides. I. Research design,
informatics, and results on d(CpG) steps," Biophys. J. 87, 3799-3813.
T. E. Cheatham, III "Simulation and modeling of nucleic acid
structure, dynamics and interactions."
Curr. Opin. Struct. Biol. 14, 360-367 (2004)
F. Lankas, J. Sponer, J. Langowski, and T. E. Cheatham, III. "DNA
deformability at the base pair level.". J. Amer. Chem. Soc.
126, 4124-4125 (2004).
E. Fadrna, N. Spackova, R. Stefl, J. Koca, T. E. Cheatham, III, and
J. Sponer. "Molecular dynamics simulations of guanine quadruplex
loops: Advances and force field limitations". Biophys. J. 87, 227-242
(2004)].
N. Spackova, T. E. Cheatham, III, F. Ryjacek, F. Lankas, L. van
Meervelt, P. Hobza, and J. Sponer. "Molecular dynamics simulations
and thermodynamics analysis of DNA-drug complexes. Minor groove
binding between 4.-6-diamino-2-phenylindole and DNA duplexes in
solution". J. Amer. Chem. Soc. 125, 1759-1769 (2003).
R. Stefl, T. E. Cheatham, III, N. Spackova, E. Fadrna, I. Berger,
J. Koca, and J. Sponer. "Formation pathways of a guanine-quadruplex DNA
revealed by molecular dynamics and thermodynamical analysis of the
substates". Biophys. J. 85, 1787-1804 (2003).
J. P. Lewis, T. E. Cheatham, III, H. Wang, E. Starikow, and
O. F. Sankey. "Dynamically amorphous character of electronic states in
poly(dA)-poly(dT) DNA". J. Phys. Chem. B 107, 2581-2587 (2003).
F. Lankas, J. Sponer, J. Langowski & T. E. Cheatham, III. "DNA
base-pair step deformability inferred from molecular dynamics
simulation". Biophys. J. 85, 2872-2883 (2003)
F. Lankas, T. E. Cheatham, III, P. Hobza, J. Langowski,
N. Spackova, and J. Sponer. "Critical effect of the N2 amino group on
structure, dynamics and elasticity of DNA polypurine
tracts". Biophys. J. 82, 2592-2609 (2002).
J. P. Lewis, J. Pikus, T. E. Cheatham, III, E. B. Starikov,
H. Wang, J. Tomfohr, and O. F. Sankey. "A comparison of electronic
states in periodic and aperiodic poly(dA)-poly(dT) DNA".
Phys. Stat. Sol. (b) 233, 90-100 (2002).
T. E. Cheatham, III and M. A. Young. "Molecular dynamics
simulations of nucleic acids: Successes, limitations and promise".
Biopolyers Nuc. Acid Sci. 56, 232-256 (2001).
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman.
"Molecular modeling of nucleic acid structure" in
Current Protocols in Nucleic Acid Chemistry6(1): 7.5.1-7.5.12.
Wiley: New York (2001).
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular
modeling of nucleic acid structure: Energy and sampling" in Current
Protocols in Nucleic Acid Chemistry. (Wiley: New York) 4(1): 7.8.1-7.8.20
(2001)
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular
modeling of nucleic acid structure: Electrostatics and solvation" in
Current Protocols in Nucleic Acid Chemistry. (Wiley: New York)
5(1): 7.9.1-7.9.21 (2001).
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular
modeling of nucleic acid structure: Setup and analysis" in Current
Protocols in Nucleic Acid Chemistry. (Wiley: New York) 6(1): 7.10.1-7.10.17
(2001).
T. E. Cheatham, III & P. A. Kollman. "Molecular dynamics simulations
of nucleic acids" in Ann. Rev. Phys. Chem. 51, 434-471
(2000).
P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong,
M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak,
J. Srinivasan, D. A. Case & T. E. Cheatham, III. "Calculating
structures and free energies of complex molecules: Combining molecular
mechanics and continuum models." Acc. Chem. Res. 33, 889-897 (2000).
T. E. Cheatham, P. Cieplak & P. A. Kollman.
"A modified version of the Cornell et al. force field with improved
sugar pucker phases and helical repeat."
J. Biomol. Struct. Dyn. 16, 845-862 (1999).
D. E. Konerding, T. E. Cheatham, III, P. A. Kollman & T. L. James.
"Restrained molecular dynamics of solvated duplex DNA using the
particle mesh Ewald method" J. Biomol. NMR. 13, 119-131 (1999).
J. L. Miller, T. E. Cheatham, III, & P. A. Kollman. "Simulation of
Nucleic Acid Structure." Oxford Handbook of Nucleic Acid Structure
S. Neidle, editor; Oxford University Press, pp. 95-115 (1999).
M. F. Crowley, T. A. Darden, T. E. Cheatham, III & D. Deerfield.
"Fine- and coarse-grain parallel AMBER and particle mesh Ewald on
MPP's" in Parallel Computing for Industrial and Scientific
Applications, Eds: J. Jenness (Morgan-Kaufmann) (1999).
T. E. Cheatham, III & B. R. Brooks.
"Recent advances in molecular dynamics simulation towards realistic
representation of biomolecules in solution".
Theor. Chem. Acc. 99, 279-288 (1998).
T. E. Cheatham, J. Srinivasan, D. A. Case & P. A. Kollman.
"Molecular dynamics and continuum solvent studies of the stability
of polyG-polyC and polyA-polyT DNA duplexes in solution."
J. Biomol. Struct. Dyn. 16, 265-280 (1998).
T. E. Cheatham, III & P. A. Kollman. "Molecular dynamics simulation
of nucleic acids in solution: How sensitive are the results to small
perturbations in the force field and environment?" in Structure,
Motion, Interactions and Expression of Biological Macromolecules,
Proceedings of the 10th Conversation. Eds: R.H. Sarma & M.H. Sarma
(Adenine Press) p. 99-116 (1998).
T. E. Cheatham, III, J. L. Miller, T. I. Spector, P. Cieplak &
P. A. Kollman.
"Molecular dynamics simulations on nucleic acid systems using the
Cornell et al. force field and particle mesh Ewald electrostatics."
in Modeling and Structure Determination of Nucleic Acids. Eds:
N.B. Leontis & J. Santa Lucia Jr (ACS: Washington, DC) p. 285-303 (1998).
S. Bogusz, T. E. Cheatham, III & B. R. Brooks.
"Removal of pressure and free energy artifacts in charged periodic systems
via net charged corrections to the Ewald potential."
J. Chem. Phys. 108, 7070-7084 (1998).
J. Srinivasan, T. E. Cheatham, III, P. Cieplak, P. A. Kollman &
D. A. Case. "Continuum solvent studies of the stability of DNA, RNA
and phosphoramidate-DNA helices." J. Amer. Chem. Soc. 120, 9401-9409
(1998).
S. C. Harvey, R. K.-Z. Tan & T. E. Cheatham, III.
"The flying ice cube: Velocity rescaling in molecular dynamics leads to
violation of energy equipartition."
J. Comp. Chem.19, 726-740 (1998).
P. A. Kollman, D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross,
T. E. Cheatham, III, S. DeBolt, D. M. Ferguson & G . Seibel. "AMBER"
in Encyclopedia of Computational Chemistry
Wiley-Interscience:NY (1998).
M. Hodoscek, E. M. Billings, T. E. Cheatham, III & B. R. Brooks.
"High performance computing in biophysics: Recent experiences and
developments of CHARMM." Proceedings of the International Symposium
on Supercomputing: New Horizons of Computational Science. Kluwer
Academic (1998).
T. E. Cheatham, III, J. L. Miller, T. I. Spector, P. Cieplak &
P. A. Kollman. "Molecular dynamics simulations on nucleic acid
systems using the Cornell et al. force field and particle mesh Ewald
electrostatics." in Modeling and Structure Determination of Nucleic
Acids, ACS Symposium Series No. 682. Leontis, NB & Santa Lucia, Jr J,
editors. p 285-303 (1998).
T.E. Cheatham, III & P.A. Kollman.
"Insight into the stabilization of A-DNA by specific ion
association: Spontaneous B-DNA to A-DNA transitions observed in molecular
dynamics simulations of d[ACCCGCGGGT]2 in the presence of
hexaamminecobalt(III)."
Structure 5, 1297-1311 (1997).
T.E. Cheatham, III, M.F. Crowley, T. Fox & P.A. Kollman.
"A molecular level picture of the stabilization of A-DNA in mixed
ethanol-water solutions"
Proc. Natl. Acad. Sci. 94, 9626-9630 (1997).
T.E. Cheatham, III & P. A. Kollman.
"Molecular dynamics simulations highlight the
structural differences among DNA:DNA, RNA:RNA and
DNA:RNA hybrid duplexes"
J. Amer. Chem. Soc. (1997) 119 4805-4825.
P. Cieplak, T.E. Cheatham, III & P.A. Kollman.
"Molecular dynamics simulations find that 3' phosphoramidate
modified DNA duplexes undergo a B to A transition and normal DNA
duplexes an A to B transition."
J. Amer. Chem. Soc. 119, 6722-6730 (1997).
T. Spector, T. E. Cheatham, III & P.A. Kollman.
"Unrestrained molecular dynamics of photodamaged DNA in aqueous solution."
J. Amer. Chem. Soc. 119, 7095-7104 (1997).
M. F. Crowley, T. A. Darden, T. E. Cheatham, III & D. Deerfield.
"Adventures in improving the scaling and accuracy of a parallel
molecular dynamics program." J. Supercomputing 11(3),
255-278 (1997)
T. A. Darden, L. G. Pedersen, A. Y. Toukmaji, M. F. Crowley &
T. E. Cheatham, III. "Particle-mesh based methods for fast Ewald
summation in molecular dynamics simulations". Proceedings of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing. M. Heath et al., editors. Minn, MN. March (1997).
T.E. Cheatham, III & P.A. Kollman.
"Observation of the A DNA to B DNA transition during
unrestrained molecular dynamics in aqueous solution."
J. Mol. Biol. 259:(3), 434-444 (1996).
T.E. Cheatham, III, J.L. Miller, T. Fox, T.A. Darden and
P.A. Kollman. "Molecular dynamics simulations on solvated
biomolecular systems: The Particle Mesh Ewald method leads to
stable trajectories of DNA, RNA, and proteins."
J. Amer. Chem. Soc. 117, 4193 (1995).
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross,
T.E. Cheatham III, S. DeBolt, D.M. Ferguson,
G.L. Seibel and P.A. Kollman. "AMBER, a package of computer
programs for applying molecular mechanics, normal mode
analysis, molecular dynamics and free energy calculations to
simulate the structural and energetic properties of molecules."
Computer Physics Communications, 91, 1-41. (1995)
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