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1

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

zhang, changsheng, Lu, Chao, Jing, Zhifeng, Wu, Chuanjie, Piquemal, Jean-Philip, Ponder, Jay William, Ren, Pengyu

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 5.69 MB

english, 2018

2

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Harger, Matthew, Li, Daniel, Wang, Zhi, Dalby, Kevin, Lagardère, Louis, Piquemal, Jean-Philip, Ponder, Jay, Ren, Pengyu

Journal:

Journal of Computational Chemistry

Year:

2017

Language:

english

File:

PDF, 635 KB

english, 2017

3

Tinker 8: Software Tools for Molecular Design

Rackers, Joshua A, Wang, Zhi, Lu, Chao, Laury, Marie L, Lagardere, Louis, Schnieders, Michael J, Piquemal, Jean-Philip, Ren, Pengyu, Ponder, Jay William

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 5.14 MB

english, 2018

4

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

Pengyu Ren, Jay W. Ponder

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 136 KB

english, 2002

5

Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics

Jianyun Lu, Chan-Lan Lin, Changguo Tang, Jay W Ponder, Jeff L.F Kao, David P Cistola, Ellen Li

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 609 KB

english, 2000

6

Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

Pappu, Rohit V., Hart, Reece K., Ponder, Jay W.

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 288 KB

english, 1998

7

Synthesis of 4-methyl-3-heptanol and 4-methyl-3-heptanone. Two easily synthesized insect pheromones

Einterz, Robert M., Ponder, Jay W., Lenox, Ronald S.

Journal:

Journal of Chemical Education

Year:

1977

Language:

english

File:

PDF, 1.60 MB

english, 1977

8

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field

Laury, Marie L., Wang, Zhi, Gordon, Aaron S., Ponder, Jay W.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2018

Language:

english

File:

PDF, 965 KB

english, 2018

9

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

Dudek, Michael J., Ramnarayan, K., Ponder, Jay W.

Journal:

Journal of Computational Chemistry

Year:

1998

Language:

english

File:

PDF, 667 KB

english, 1998

10

Exploring the similarities between potential smoothing and simulated annealing

Hart, Reece K., Pappu, Rohit V., Ponder, Jay W.

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 438 KB

english, 2000

11

Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods

Enoch S. Huang, Patrice Koehl, Michael Levitt, Rohit V. Pappu, Jay W. Ponder

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 212 KB

english, 1998

12

Multipole electrostatics in hydration free energy calculations

Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Ren

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 241 KB

english, 2011

13

An efficient newton-like method for molecular mechanics energy minimization of large molecules

Jay W. Ponder, Frederic M. Richards

Journal:

Journal of Computational Chemistry

Year:

1987

Language:

english

File:

PDF, 856 KB

english, 1987

14

Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization

Craig E. Kundrot, Jay W. Ponder, Frederic M. Richards

Journal:

Journal of Computational Chemistry

Year:

1991

Language:

english

File:

PDF, 713 KB

english, 1991

15

Accurate modeling of the intramolecular electrostatic energy of proteins

Michael J. Dudek, Jay W. Ponder

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 2.21 MB

english, 1995

16

Synthesis of a stable analog of thromboxane A2 with methylene replacing the 9,11-bridging oxygen

E.J. Corey, Jay W. Ponder, Peter Ulrich

Journal:

Tetrahedron Letters

Year:

1980

Language:

english

File:

PDF, 253 KB

english, 1980

17

The stereochemistry and biosynthesis of hybridalactone, an eicosanoid from laurencia hybrida

E.J. Corey, Biswanath De, Jay W. Ponder, Jeremy M. Berg

Journal:

Tetrahedron Letters

Year:

1984

Language:

english

File:

PDF, 276 KB

english, 1984

18

Stereochemistry of the hygrolidins

E.J. Corey, Jay W. Ponder

Journal:

Tetrahedron Letters

Year:

1984

Language:

english

File:

PDF, 262 KB

english, 1984

19

Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures

Enoch S. Huang, Jay W. Ponder, Ram Samudrala

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 3.08 MB

english, 1998

20

Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization

Thomas D. Rasmussen, Pengyu Ren, Jay W. Ponder, Frank Jensen

Journal:

International Journal of Quantum Chemistry

Year:

2007

Language:

english

File:

PDF, 95 KB

english, 2007

21

10.1038/4922

Ponder, Jay W., Pappu, Rohit V., Marshall, Garland R.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 346 KB

english, 1999

22

10.1038/5891

Pappu, Rohit V., Marshall, Garland R., Ponder, Jay W.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 45 KB

english, 1999

23

MSCALE: A General Utility for Multiscale Modeling

Woodcock, H. Lee, Miller, Benjamin T., Hodoscek, Milan, Okur, Asim, Larkin, Joseph D., Ponder, Jay W., Brooks, Bernard R.

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 3.41 MB

english, 2011

24

Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field

Grossfield, Alan, Ren, Pengyu, Ponder, Jay W.

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 133 KB

english, 2003

25

Molecular Dynamics of β-Hairpin Models of Epigenetic Recognition Motifs

Zheng, Xiange, Wu, Chuanjie, Ponder, Jay W., Marshall, Garland R.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

26

Crystallization and Initial X-ray Crystallographic Characterization of Recombinant Bovine Inositol Polyphosphate 1-Phosphatase Produced in Spodoptera frugiperda Cells

John D. York, Zhi-wei Chen, Jay W. Ponder, Anil K. Chauhan, F.Scott Mathews, Philip W. Majerus

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 444 KB

1994

27

The NMR Solution Structure of Intestinal Fatty Acid-binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm

Michael E. Hodsdon, Jay W. Ponder, David P. Cistola

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 504 KB

english, 1996

28

The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure

Jianyun Lu, Chan-Lan Lin, Changguo Tang, Jay W. Ponder, Jeff L.F. Kao, David P. Cistola, Ellen Li

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 1.15 MB

english, 1999

29

Ab Initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions

Enoch S. Huang, Ram Samudrala, Jay W. Ponder

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 383 KB

english, 1999

30

From Data or Dogma? The Myth of the Ideal Helix

Kuster, Daniel J., Urahata, Sergio, Ponder, Jay W., Marshall, Garland R.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 38 KB

english, 2009

31

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Ren, Pengyu, Ponder, Jay W.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 166 KB

english, 2003

32

[Advances in Protein Chemistry] Protein Simulations Volume 66 || Force Fields for Protein Simulations

Year:

2003

Language:

english

File:

PDF, 671 KB

english, 2003

33

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

Xiang, Jin Yu, Ponder, Jay W.

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 715 KB

english, 2013

34

Tertiary templates for proteins

Ponder, Jay W., Richards, Frederic M.

Journal:

Journal of Molecular Biology

Year:

1987

Language:

english

File:

PDF, 2.11 MB

english, 1987

35

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

Shi, Yue, Xia, Zhen, Zhang, Jiajing, Best, Robert, Wu, Chuanjie, Ponder, Jay W., Ren, Pengyu

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.55 MB

english, 2013

36

Systematic Improvement of a Classical Molecular Model of Water

Wang, Lee-Ping, Head-Gordon, Teresa, Ponder, Jay W., Ren, Pengyu, Chodera, John D., Eastman, Peter K., Martinez, Todd J., Pande, Vijay S.

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.91 MB

english, 2013

37

Systematic Improvement on the Classical Molecular Model of Water

Wang, Lee-Ping, Head-Gordon, Teresa, Ponder, Jay, Ren, Pengyu, Chodera, John, Eastman, Peter, Martinez, Todd J., Pande, Vijay S.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 57 KB

english, 2014

38

Light-Activated Rhodopsin Induces Structural Binding Motif in G Protein α Subunit

Oleg G. Kisselev, Jeff Kao, Jay W. Ponder, Yang C. Fann, N. Gautam and Garland R. Marshall

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 1.68 MB

english, 1998

39

Current Status of the AMOEBA Polarizable Force Field

Ponder, Jay W., Wu, Chuanjie, Ren, Pengyu, Pande, Vijay S., Chodera, John D., Schnieders, Michael J., Haque, Imran, Mobley, David L., Lambrecht, Daniel S., DiStasio, Robert A., Head-Gordon, Martin, Cl

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 623 KB

english, 2010

40

Temperature and Pressure Dependence of the AMOEBA Water Model

Ren, Pengyu, Ponder, Jay W.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 195 KB

english, 2004

41

Crystal Structure of Inositol Polyphosphate 1-Phosphatase at 2.3-.ANG. Resolution

York, John D., Ponder, Jay W., Chen, Z., Mathews, F. Scott, Majerus, Philip W.

Journal:

Year:

1994

Language:

english

File:

PDF, 2.28 MB

english, 1994

42

Metal-ammonia reduction of triptycene and related benzobarrelene derivatives

Rabideau, Peter W., Jessup, Donald W., Ponder, Jay W., Beekman, George F.

Journal:

Journal of Organic Chemistry

Year:

1979

Language:

english

File:

PDF, 531 KB

english, 1979

43

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Ren, Pengyu, Wu, Chuanjie, Ponder, Jay W.

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.69 MB

english, 2011

44

Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum

Schnieders, Michael J., Ponder, Jay W.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 155 KB

english, 2007

45

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

Xiang, Jin Yu, Ponder, Jay W.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.73 MB

english, 2014

46

Calculation of the reaction field due to off-center point multipoles

Kong, Yong, Ponder, Jay W.

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 502 KB

english, 1997

47

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

Laury, Marie L., Wang, Lee-Ping, Pande, Vijay S., Head-Gordon, Teresa, Ponder, Jay W.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.80 MB

english, 2015

48

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

Wang, Qiantao, Rackers, Joshua A., He, Chenfeng, Qi, Rui, Narth, Christophe, Lagardere, Louis, Gresh, Nohad, Ponder, Jay W., Piquemal, Jean-Philip, Ren, Pengyu

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.32 MB

english, 2015

49

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

Schnieders, Michael J., Baker, Nathan A., Ren, Pengyu, Ponder, Jay W.

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 278 KB

english, 2007

50

Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field

Bell, David R., Qi, Rui, Jing, Zhifeng, Xiang, Jin Yu, Mejias, Christopher, Schnieders, Michael J., Ponder, Jay W., Ren, Pengyu

Journal:

Physical Chemistry Chemical Physics

Year:

2016

Language:

english

File:

PDF, 2.54 MB

english, 2016