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1

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

David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham III, Steve DeBolt, David Ferguson, George Seibel, Peter Kollman

Journal:

Computer Physics Communications

Year:

1995

Language:

english

File:

PDF, 2.84 MB

english, 1995

2

Free energy calculations: Applications to chemical and biochemical phenomena

Kollman, Peter.

Journal:

Chemical Reviews

Year:

1993

Language:

english

File:

PDF, 3.96 MB

english, 1993

3

Does Federalism Really Matter?

Erk, Jan, Gibson, Edward L., Amoretti, Ugo M., Bermeo, Nancy, Noël, Alain, Kelemen, R. Daniel, Filippov, Mikhail, Ordeshook, Peter C., Shvetsova, Olga, Chhibber, Pradeep, Kollman, Ken

Journal:

Comparative Politics

Year:

2006

Language:

english

File:

PDF, 2.23 MB

english, 2006

4

Development and testing of a general amber force field

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 320 KB

english, 2004

5

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field"Journal of Computational Chemistry(2004) 25(9) 1157–1174

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case

Journal:

Journal of Computational Chemistry

Year:

2005

File:

PDF, 34 KB

2005

6

Use of restrained molecular dynamics in water to determine three-dimensional protein structure: Prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II

Laurent Chiche, Christine Gaboriaud, Annie Heitz, Jean-Paul Mornon, Bertrand Castro, Peter A. Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1989

Language:

english

File:

PDF, 1.05 MB

english, 1989

7

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J . Am . Chem . Soc . 1995 , 117 , 5179−5197

Cornell, Wendy D., Cieplak, Piotr, Bayly, Christopher I., Gould, Ian R., Merz, Kenneth M., Ferguson, David M., Spellmeyer, David C., Fox, Thomas, Caldwell, James W., Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1996

Language:

english

File:

PDF, 27 KB

english, 1996

8

What determines the van der Waals coefficient β in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?

Wei Wang, Jian Wang, Peter A. Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 111 KB

english, 1999

9

A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease

Piotr Cieplak, Peter A. Kollman

Journal:

Journal of Molecular Recognition

Year:

1996

Language:

english

File:

PDF, 645 KB

english, 1996

10

Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers

Peter A. Kollman, Paul K. Weiner, Andrew Dearing

Journal:

Year:

1981

Language:

english

File:

PDF, 1.55 MB

english, 1981

11

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

Paul K. Weiner, Peter A. Kollman

Journal:

Journal of Computational Chemistry

Year:

1981

Language:

english

File:

PDF, 1.37 MB

english, 1981

12

Atomic charges derived from semiempirical methods

Brent H. Besler, Kenneth M. Merz Jr., Peter A. Kollman

Journal:

Journal of Computational Chemistry

Year:

1990

Language:

english

File:

PDF, 788 KB

english, 1990

13

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

Shuichi Miyamoto, Peter A. Kollman

Journal:

Journal of Computational Chemistry

Year:

1992

Language:

english

File:

PDF, 890 KB

english, 1992

14

Recent Advances in Structure-Based Ligand Design Using Molecular Dynamics and Monte Carlo Methods

Journal:

Pharmaceutical Research

Year:

1998

File:

PDF, 222 KB

1998

15

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Cornell, Wendy D., Cieplak, Piotr, Bayly, Christopher I., Gould, Ian R., Merz, Kenneth M., Ferguson, David M., Spellmeyer, David C., Fox, Thomas, Caldwell, James W., Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1995

Language:

english

File:

PDF, 2.21 MB

english, 1995

16

Theory of the hydrogen bond

Kollman, Peter A., Allen, Leland C.

Journal:

Chemical Reviews

Year:

1972

Language:

english

File:

PDF, 2.52 MB

english, 1972

17

BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

Wang, Wei, Donini, Oreola, Reyes, Carolina M., Kollman, Peter A.

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

2001

Language:

english

File:

PDF, 331 KB

english, 2001

18

Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design

Huo, Shuanghong, Wang, Junmei, Cieplak, Piotr, Kollman, Peter A., Kuntz, Irwin D.

Journal:

Journal of Medicinal Chemistry

Year:

2002

Language:

english

File:

PDF, 297 KB

english, 2002

19

Molecular dynamics in the endgame of protein structure prediction

Matthew R. Lee, Jerry Tsai, David Baker, Peter A. Kollman

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 814 KB

english, 2001

20

Quantitative relations between steroid structure and binding to putative progesterone receptors

Lee, David L., Kollman, Peter A., Marsh, Fred J., Wolff, Manfred E.

Journal:

Journal of Medicinal Chemistry

Year:

1977

Language:

english

File:

PDF, 1.01 MB

english, 1977

21

A theoretical study of intramolecular hydrogen bonding in ortho-substituted phenols and thiophenols

Dietrich, Stephen W., Jorgensen, Eugene C., Kollman, Peter A., Rothenberg, Steve

Journal:

Journal of the American Chemical Society

Year:

1976

Language:

english

File:

PDF, 1.77 MB

english, 1976

22

Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models

Kuhn, Bernd, Kollman, Peter A.

Journal:

Journal of Medicinal Chemistry

Year:

2000

Language:

english

File:

PDF, 61 KB

english, 2000

23

Are time-averaged restraints necessary for nuclear magnetic resonance refinement?: A model study for DNA

David A. Pearlman, Peter A. Kollman

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 9.91 MB

english, 1991

24

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

Bayly, Christopher I., Cieplak, Piotr, Cornell, Wendy, Kollman, Peter A.

Journal:

Journal of Physical Chemistry

Year:

1993

Language:

english

File:

PDF, 3.54 MB

english, 1993

25

A new force field for molecular mechanical simulation of nucleic acids and proteins

Weiner, Scott J., Kollman, Peter A., Case, David A., Singh, U. Chandra, Ghio, Caterina, Alagona, Guliano, Profeta, Salvatore, Weiner, Paul

Journal:

Journal of the American Chemical Society

Year:

1984

Language:

english

File:

PDF, 2.74 MB

english, 1984

26

Calculation of free energy changes in ion–water clusters using nonadditive potentials and the Monte Carlo method

Cieplak, Piotr, Lybrand, Terry P., Kollman, Peter A.

Journal:

The Journal of Chemical Physics

Year:

1987

Language:

english

File:

PDF, 1.06 MB

english, 1987

27

Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?

Kollman, Peter A., Kuhn, Bernd, Peräkylä, Mikael

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 58 KB

english, 2002

28

New-Generation Amber United-Atom Force Field

Yang, Lijiang, Tan, Chun-hu, Hsieh, Meng-Juei, Wang, Junmei, Duan, Yong, Cieplak, Piotr, Caldwell, James, Kollman, Peter A., Luo, Ray

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 450 KB

english, 2006

29

A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy-perturbation methods

Cieplak, Piotr, Bash, Paul, Singh, U. Chandra, Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1987

Language:

english

File:

PDF, 859 KB

english, 1987

30

An approach to the application of free energy perturbation methods using molecular dynamics: applications to the transformations of methanol .fwdarw. ethane, oxonium .fwdarw. ammonium, glycine .fwdarw. alanine, and alanine .fwdarw. phenylalanine in aqueous solution and to H3O+(H2O)3 .fwdarw. NH4+(H2O)3 in the gas phase

Singh, U. C., Brown, Frank K., Bash, Paul A., Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

1987

Language:

english

File:

PDF, 1012 KB

english, 1987

31

Investigation of Neuraminidase-Substrate Recognition Using Molecular Dynamics and Free Energy Calculations

Masukawa, Kevin M., Kollman, Peter A., Kuntz, Irwin D.

Journal:

Journal of Medicinal Chemistry

Year:

2003

Language:

english

File:

PDF, 194 KB

english, 2003

32

Theoretical calculations of hydrolysis energies of "high-energy" molecules. 3. Theoretical calculations on the geometric destabilization of 3',5'- and 2',3'-cyclic nucleotides

Marsh, Frederick J., Weiner, Paul, Douglas, John E., Kollman, Peter A., Kenyon, George L., Gerlt, John A.

Journal:

Journal of the American Chemical Society

Year:

1980

Language:

english

File:

PDF, 771 KB

english, 1980

33

Water–water and water–ion potential functions including terms for many body effects

Lybrand, Terry P., Kollman, Peter A.

Journal:

The Journal of Chemical Physics

Year:

1985

Language:

english

File:

PDF, 1.24 MB

english, 1985

34

Reply to: ‘‘Comment on ‘Water–water and water–ion potential functions including terms for many-body effects,’ T. P. Lybrand and P. Kollman, J. Chem. Phys. 83, 2923 (1985) and on ‘Calculation of free energy changes in ion–water clusters using nonadditive potential and the Monte Carlo methods,’ P. Cieplak, T. P. Lybrand, and P. Kollman, J. Chem. Phys. 86, 6393 (1987)’’

Kollman, Peter, Lybrand, Terry, Cieplak, Piotr

Journal:

The Journal of Chemical Physics

Year:

1988

Language:

english

File:

PDF, 307 KB

english, 1988

35

An analysis of the hard-soft Lewis acid-base concept and the Drago equation employing ab initio molecular orbital theory

Douglas, John, Kollman, Peter

Journal:

Journal of Physical Chemistry

Year:

1981

Language:

english

File:

PDF, 817 KB

english, 1981

36

Decisions in Force Field Development: An Alternative to Those Described by Roterman et al.

Kollman, Peter A., Dill, Kenneth A.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1991

Language:

english

File:

PDF, 329 KB

english, 1991

37

Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions

Chipot, Christophe, Kollman, Peter A., Pearlman, David A.

Journal:

Journal of Computational Chemistry

Year:

1996

Language:

english

File:

PDF, 1.71 MB

english, 1996

38

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics

Cornell, Wendy D., Ha, Maria P., Sun, Yax, Kollman, Peter A.

Journal:

Journal of Computational Chemistry

Year:

1996

Language:

english

File:

PDF, 666 KB

english, 1996

39

Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes

Radmer, Randall J., Kollman, Peter A.

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 228 KB

english, 1997

40

Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics

Dixon, Richard W., Kollman, Peter A.

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 203 KB

english, 1997

41

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”?

Fox, Thomas, Kollman, Peter A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 1.73 MB

english, 1996

42

Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods

Lu Wang, David L. Veenstra, Randall J. Radmer, Peter A. Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 373 KB

english, 1998

43

Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study

Jian Wang, Richard Dixon, Peter A. Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 195 KB

english, 1999

44

Flexible ligand docking: A multistep strategy approach

Jian Wang, Peter A. Kollman, Irwin D. Kuntz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 414 KB

english, 1999

45

The free energies for mutating S27 and W79 to alanine in streptavidin and its biotin complex: The relative size of polar and nonpolar free energies on biotin binding

Richard W. Dixon, Peter Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 30 KB

english, 1999

46

Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece

Matthew R. Lee, Yong Duan, Peter A. Kollman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 1.47 MB

english, 2000

47

Introduction: Theoretical chemistry in biology: From molecular structure to functional mechanisms

Peter Kollman, Harel Weinstein, Michael Zerner

Journal:

International Journal of Quantum Chemistry

Year:

1998

Language:

english

File:

PDF, 63 KB

english, 1998

48

Molecular dynamics simulations can reproduce the subtle differences in NADP and NHDP binding to isocitrate dehydrogenase

Mireia Garcia-Viloca, Peter A. Kollman

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 314 KB

english, 1999

49

Molecular dynamics simulation studies of liquid acetonitrile: New six-site model

Xavier Grabuleda, Carlos Jaime, Peter A. Kollman

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 252 KB

english, 2000

50

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

Junmei Wang, Piotr Cieplak, Peter A. Kollman

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 357 KB

english, 2000

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