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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

[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

3

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

4

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

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

Foreword

Adrian Roitberg, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 23 KB

english, 2004

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments

Ding, Fangyu, Layten, Melinda, Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 318 KB

english, 2008

26

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

Wickstrom, Lauren, Okur, Asim, Simmerling, Carlos

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 137 KB

english, 2009

27

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model

Geney, Raphaël, Layten, Melinda, Gomperts, Roberto, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 614 KB

english, 2006

28

Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models

Okur, Asim, Wickstrom, Lauren, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 303 KB

english, 2008

29

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Simmerling, Carlos, Strockbine, Bentley, Roitberg, Adrian E.

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 96 KB

english, 2002

30

Modified Replica Exchange Simulation Methods for Local Structure Refinement

Cheng, Xiaolin, Cui, Guanglei, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 789 KB

english, 2005

31

Drug Pressure Selected Mutations in HIV-1 Protease Alter Flap Conformations

Galiano, Luis, Ding, Fangyu, Veloro, Angelo M., Blackburn, Mandy E., Simmerling, Carlos, Fanucci, Gail E.

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 435 KB

english, 2009

32

Reconciling the Solution and X-ray Structures of the Villin Headpiece Helical Subdomain: Molecular Dynamics Simulations and Double Mutant Cycles Reveal a Stabilizing Cation−π Interaction †

Wickstrom, Lauren, Bi, Yuan, Hornak, Viktor, Raleigh, Daniel P., Simmerling, Carlos

Journal:

Year:

2007

Language:

english

File:

PDF, 679 KB

english, 2007

33

Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation

Roe, Daniel R., Okur, Asim, Wickstrom, Lauren, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 235 KB

english, 2007

34

CoA Adducts of 4-Oxo-4-phenylbut-2-enoates: Inhibitors of MenB from the M. tuberculosis Menaquinone Biosynthesis Pathway

Li, Xiaokai, Liu, Nina, Zhang, Huaning, Knudson, Susan E., Li, Huei-Jiun, Lai, Cheng-Tsung, Simmerling, Carlos, Slayden, Richard A., Tonge, Peter J.

Journal:

ACS Medicinal Chemistry Letters

Year:

2011

Language:

english

File:

PDF, 2.60 MB

english, 2011

35

The Open Structure of a Multi-Drug-Resistant HIV-1 Protease is Stabilized by Crystal Packing Contacts

Layten, Melinda, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 164 KB

english, 2006

36

Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase

Bergonzo, Christina, Campbell, Arthur J., de los Santos, Carlos, Grollman, Arthur P., Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 1.61 MB

english, 2011

37

A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA

Li, Huei-Jiun, Lai, Cheng-Tsung, Pan, Pan, Yu, Weixuan, Liu, Nina, Bommineni, Gopal R., Garcia-Diaz, Miguel, Simmerling, Carlos, Tonge, Peter J.

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 4.20 MB

english, 2014

38

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies

Song, Kun, Campbell, Arthur J., Bergonzo, Christina, de los Santos, Carlos, Grollman, Arthur P., Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 2.09 MB

english, 2009

39

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

Luchko, Tyler, Gusarov, Sergey, Roe, Daniel R., Simmerling, Carlos, Case, David A., Tuszynski, Jack, Kovalenko, Andriy

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 4.02 MB

english, 2010

40

Improved Generalized Born Solvent Model Parameters for Protein Simulations

Nguyen, Hai, Roe, Daniel R., Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.04 MB

english, 2013

41

HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State

Hornak, Viktor, Okur, Asim, Rizzo, Robert C., Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 118 KB

english, 2006

42

Molecular Simulations Reveal a Common Binding Mode for Glycosylase Binding of Oxidatively Damaged DNA Lesions

Song, Kun, Kelso, Catherine, de los Santos, Carlos, Grollman, Arthur P., Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 101 KB

english, 2007

43

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

Nguyen, Hai, Maier, James, Huang, He, Perrone, Victoria, Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

44

Combined Locally Enhanced Sampling and Particle Mesh Ewald as a Strategy To Locate the Experimental Structure of a Nonhelical Nucleic Acid

Simmerling, Carlos, Miller, Jennifer L., Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 153 KB

english, 1998

45

Generalized Born Model with a Simple, Robust Molecular Volume Correction

Mongan, John, Simmerling, Carlos, McCammon, J. Andrew, Case, David A., Onufriev, Alexey

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 549 KB

english, 2007

46

Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir

Roitberg, Adrian E., Okur, Asim, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 117 KB

english, 2007

47

Hydrophobic "Collapse" in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in Water

Simmerling, Carlos, Elber, Ron

Journal:

Journal of the American Chemical Society

Year:

1994

Language:

english

File:

PDF, 2.06 MB

english, 1994

48

Structural Transitions of Transmembrane Helix 6 in the Formation of Metarhodopsin I

Eilers, Markus, Goncalves, Joseph A., Ahuja, Shivani, Kirkup, Colleen, Hirshfeld, Amiram, Simmerling, Carlos, Reeves, Philip J., Sheves, Mordechai, Smith, Steven O.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 3.30 MB

english, 2012

49

Inhibitor-Induced Conformational Shifts and Ligand-Exchange Dynamics for HIV-1 Protease Measured by Pulsed EPR and NMR Spectroscopy

Huang, Xi, de Vera, Ian Mitchelle S., Veloro, Angelo M., Blackburn, Mandy E., Kear, Jamie L., Carter, Jeffery D., Rocca, James R., Simmerling, Carlos, Dunn, Ben M., Fanucci, Gail E.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 2.75 MB

english, 2012

50

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

Okur, Asim, Roe, Daniel R., Cui, Guanglei, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 234 KB

english, 2007

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