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1

The Amber biomolecular simulation programs

David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 587 KB

english, 2005

2

Normal Functioning and the Treatment/Enhancement Distinction: An Opportunity Based Assessment

Huggins, Jonathan, Simmerling, Mary

Journal:

Journal of Religion and Health

Year:

2014

Language:

english

File:

PDF, 154 KB

english, 2014

3

Ökonomie. Prognostik und Desaster

Simmerl, Georg, Vogl, Joseph

Journal:

Year:

2017

Language:

german

File:

PDF, 111 KB

german, 2017

4

An Offering of Hope During COVID-19: A Personal Reflection

Simmerling, Mary

Journal:

Journal of Religion and Health

Year:

2020

File:

PDF, 632 KB

2020

5

High-Speed Quantum Random Number Generation Using CMOS Photon Counting Detectors

Tisa, Simone, Villa, Federica, Giudice, Andrea, Simmerle, Georg, Zappa, Franco

Journal:

IEEE Journal of Selected Topics in Quantum Electronics

Year:

2015

Language:

english

File:

PDF, 3.09 MB

english, 2015

6

Poems in memoriam

Simmerling, Mary

Journal:

Journal of Religion and Health

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

7

[WORLD SCIENTIFIC Proceedings of the International School of Physics - LERICI, Villa Marigola (7 – 18 July 1997)] Classical and Quantum Dynamics in Condensed Phase Simulations - Dynamics of peptide folding

ELBER, RON, MOHANTY, DEBASISA, SIMMERLING, CARLOS

Language:

english

File:

PDF, 1.87 MB

english

8

Advances in free-energy-based simulations of protein folding and ligand binding

Perez, Alberto, Morrone, Joseph A, Simmerling, Carlos, Dill, Ken A

Journal:

Current Opinion in Structural Biology

Year:

2016

Language:

english

File:

PDF, 761 KB

english, 2016

9

Rhetorical functions of a 'language of uncertainty' in the mass media

Simmerling, A., Janich, N.

Journal:

Public Understanding of Science

Year:

2015

Language:

english

File:

PDF, 715 KB

english, 2015

10

Assessing Incidence of Sexual Assault (SA) and Needs of SA Survivors Via Random Digit Dialing

Mary Simmerling

Journal:

Journal of Empirical Research on Human Research Ethics An International Journal

Year:

2007

Language:

english

File:

PDF, 110 KB

english, 2007

11

The commercialization of human organs for transplantation: the current status of the ethical debate

Simmerling, Mary, Angelos, Peter, Franklin, John, Abecassis, Michael

Journal:

Current Opinion in Organ Transplantation

Year:

2006

Language:

english

File:

PDF, 128 KB

english, 2006

12

PRISONERS AS ORGAN DONORS: IS IT WORTH THE EFFORT? IS IT ETHICAL?

Millis, M A., Millis, J M., Simmerling, M

Journal:

Transplantation Journal

Year:

2008

Language:

english

File:

PDF, 75 KB

english, 2008

13

Structural insights for designed alanine-rich helices: Comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation

Kun Song, James M. Stewart, R. Matthew Fesinmeyer, Niels H. Andersen, Carlos Simmerling

Journal:

Year:

2008

Language:

english

File:

PDF, 981 KB

english, 2008

14

Synthesis and Molecular Modeling of a Nitrogen Mustard DNA Interstrand Crosslink

Angelo Guainazzi, Arthur J. Campbell, Dr. Todor Angelov, Prof. Carlos Simmerling, Prof. Orlando D. Schärer

Journal:

Chemistry - A European Journal

Year:

2010

Language:

english

File:

PDF, 419 KB

english, 2010

15

ChemInform Abstract: Recent Advances in the Study of the Bioactive Conformation of Taxol

Liang Sun, Carlos Simmerling, Iwao Ojima

Journal:

Year:

2009

File:

PDF, 15 KB

2009

16

Recent Advances in the Study of the Bioactive Conformation of Taxol

Liang Sun, Carlos Simmerling, Iwao Ojima

Journal:

Year:

2009

Language:

english

File:

PDF, 1.93 MB

english, 2009

17

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 303 KB

english, 2003

18

Molecular mechanics parameters for the FapydG DNA lesion

Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 377 KB

english, 2008

19

4H-1,3,5-Oxadiazine und 4H-1,3,5-Thiadiazine aus Cyanamiden und Perhalogenketonen bzw. -thioketonen

Klaus Burger, Reinhold Simmerl

Journal:

European Journal of Organic Chemistry

Year:

1984

Language:

german

File:

PDF, 434 KB

german, 1984

20

Recipient deaths during donor surgery: A new ethical problem in living donor liver transplantation (LDLT)

Mark Siegler, Mary C. Simmerling, Jessica H. Siegler, David C. Cronin II

Journal:

Liver Transplantation

Year:

2006

Language:

english

File:

PDF, 103 KB

english, 2006

21

MOIL: A program for simulations of macromolecules

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Haiying Li, Gennady Verkhivker, Chen Keasar, Jing Zhang, Alex Ulitsky

Journal:

Computer Physics Communications

Year:

1995

Language:

english

File:

PDF, 2.28 MB

english, 1995

22

Use of the Tubulin Bound Paclitaxel Conformation for Structure-Based Rational Drug Design

Raphaël Geney, Liang Sun, Paula Pera, Ralph J. Bernacki, Shujun Xia, Susan B. Horwitz, Carlos L. Simmerling, Iwao Ojima

Journal:

Chemistry & Biology

Year:

2005

Language:

english

File:

PDF, 513 KB

english, 2005

23

Foreword

Adrian Roitberg, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 23 KB

english, 2004

24

Über Nitrierung und Denitrierung von Pektinstoffen

Hans Bock, Josef Simmerl, Max Josten

Journal:

Advanced Synthesis & Catalysis

Year:

1941

Language:

german

File:

PDF, 658 KB

german, 1941

25

Generation of accurate protein loop conformations through low-barrier molecular dynamics

Viktor Hornak, Carlos Simmerling

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 461 KB

english, 2003

26

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 695 KB

english, 2006

27

A partial nudged elastic band implementation for use with large or explicitly solvated systems

Christina Bergonzo, Arthur J. Campbell, Ross C. Walker, Carlos Simmerling

Journal:

International Journal of Quantum Chemistry

Year:

2009

Language:

english

File:

PDF, 320 KB

english, 2009

28

Der Papp-Watte-Verband

W. v. Linhart, Jul Simmerl

Journal:

Langenbeck's Archives of Surgery

Year:

1872

Language:

german

File:

PDF, 1.75 MB

german, 1872

29

Mosaic®-Bioprothese nach fünf Jahren

Walter Eichinger, Ralf Günzinger, Florian Botzenhardt, Daniela Simmerl, Brigitte Gansera, Bernhard Michael Kemkes

Journal:

Year:

2000

File:

PDF, 169 KB

2000

30

The essentialDrosophila melanogastergenewds(will die slowly) codes for a WD-repeat protein with seven repeats

M. Hollmann, E. Simmerl, U. Schäfer, M. Schäfer

Journal:

Molecular Genetics and Genomics

Year:

2002

Language:

english

File:

PDF, 633 KB

english, 2002

31

Growth and reproduction of fungal feeding Collembola as affected by fungal species, melanin and mixed diets

Stefan Scheu, Frauke Simmerling

Journal:

Year:

2004

Language:

english

File:

PDF, 151 KB

english, 2004

32

Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations

Viktor Hornak, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 353 KB

english, 2004

33

Improving the description of salt bridge strength and geometry in a Generalized Born model

Yi Shang, Hai Nguyen, Lauren Wickstrom, Asim Okur, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2011

Language:

english

File:

PDF, 1.60 MB

english, 2011

34

Inhibition of the Bacterial Enoyl Reductase FabI by Triclosan: A Structure−Reactivity Analysis of FabI Inhibition by Triclosan Analogues†

Simmerling, Carlos, Tonge, Peter J., Sivaraman, Sharada, Sullivan, Todd J., Johnson, Francis, Novichenok, Polina, Cui, Guanglei

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 153 KB

english, 2004

35

SPIE Proceedings [SPIE SPIE Defense, Security, and Sensing - Baltimore, Maryland (Monday 23 April 2012)] Advanced Photon Counting Techniques VI - High-detection efficiency and picosecond timing compact detector modules with red-enhanced SPADs

Giudice, Andrea, Simmerle, Georg, Veronese, Daniele, Biasi, Roberto, Gulinatti, Angelo, Rech, Ivan, Ghioni, Massimo, Maccagnani, Piera

Year:

2012

Language:

english

File:

PDF, 20.80 MB

english, 2012

36

Evidence for second phase transitions in the superconducting states of heavy-fermion systems and high-TC superconductors

J.P. Ströbel, M. Simmerl, H. Adrian, A. Thomä, G. Adrian, B. Hensel, G. Saemann-Ischenko

Journal:

Journal of Magnetism and Magnetic Materials

Year:

1988

Language:

english

File:

PDF, 156 KB

english, 1988

37

Targeting structural flexibility in HIV-1 protease inhibitor binding

Viktor Hornak, Carlos Simmerling

Journal:

Drug Discovery Today

Year:

2007

Language:

english

File:

PDF, 511 KB

english, 2007

38

Turbulent transport, characteristic length and time scales above and within the BEMA forest site at Castelporziano

Michael Zelger, Jan Schween, Jochen Reuder, Tullio Gori, Karin Simmerl, Ralph Dlugi

Journal:

Atmospheric Environment

Year:

1997

Language:

english

File:

PDF, 1.10 MB

english, 1997

39

Expanding Kidney Paired Donation Through Participation by Compatible Pairs

S. E. Gentry, D. L. Segev, M. Simmerling, R. A. Montgomery

Journal:

American Journal of Transplantation

Year:

2007

Language:

english

File:

PDF, 124 KB

english, 2007

40

L/I-1 Beyond coercion: a new paradigm for understanding donor motivation and informed consent in living donor transplantation (LDT)

M. Simmerling, D. Brauner

Journal:

Clinical Transplantation

Year:

2006

Language:

english

File:

PDF, 455 KB

english, 2006

41

Dynamic Behavior of DNA Base Pairs Containing 8-Oxoguanine

Cheng, Xiaolin, Kelso, Catherine, Hornak, Viktor, de los Santos, Carlos, Grollman, Arthur P., Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 677 KB

english, 2005

42

Computational Analysis of the Mode of Binding of 8-Oxoguanine to Formamidopyrimidine-DNA Glycosylase†

Song, Kun, Hornak, Viktor, de los Santos, Carlos, Grollman, Arthur P., Simmerling, Carlos

Journal:

Year:

2006

Language:

english

File:

PDF, 470 KB

english, 2006

43

Structure and regulation of a gene cluster for male accessory gland transcripts in Drosophila melanogaster

Elfriede Simmerl, Mireille Schäfer, Ulrich Schäfer

Journal:

Insect Biochemistry and Molecular Biology

Year:

1995

Language:

english

File:

PDF, 1.69 MB

english, 1995

44

Folding Cooperativity in a Three-stranded β-Sheet Model

Daniel R. Roe, Viktor Hornak, Carlos Simmerling

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 702 KB

english, 2005

45

The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure

Lauren Wickstrom, Asim Okur, Kun Song, Viktor Hornak, Daniel P. Raleigh, Carlos L. Simmerling

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

46

The Market of Human Organs: A Window Into a Poorly Understood Global Business

O.S. Surman, R. Saidi, R. Purtilo, M. Simmerling, D. Ko, T.F. Burke

Journal:

Transplantation Proceedings

Year:

2008

Language:

english

File:

PDF, 67 KB

english, 2008

47

2007: The Year of Regulatory Change

J.M. Millis, J. Huang, M.A. Millis, Y. Liu, Y. Mao, M. Simmerling

Journal:

Transplantation Proceedings

Year:

2009

Language:

english

File:

PDF, 77 KB

english, 2009

48

Prisoners as Organ Donors: Is It Worth the Effort? Is It Ethical?

M.A. Millis, M. Simmerling

Journal:

Transplantation Proceedings

Year:

2009

Language:

english

File:

PDF, 81 KB

english, 2009

49

The Mosaic bioprosthesis in the aortic position:: Hemodynamic performance after 2 years

Walter B Eichinger, Albert Schütz, Daniela Simmerl, Brigitte U Gansera, Martin Breuer, Bernhard Haslinger, Bernhard M Kemkes

Journal:

The Annals of Thoracic Surgery

Year:

1998

Language:

english

File:

PDF, 157 KB

english, 1998

50

Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose

Simmerling, Carlos, Fox, Thomas, Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 240 KB

english, 1998

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