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1

MD display: An interactive graphics program for visualization of molecular dynamics trajectories

Timothy J. Callahan, Eric Swanson, Terry P. Lybrand

Journal:

Journal of Molecular Graphics

Year:

1996

Language:

english

File:

PDF, 282 KB

english, 1996

2

Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility

Cerutti, David S., Duke, Robert E., Darden, Thomas A., Lybrand, Terry P.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 1.43 MB

english, 2009

3

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

4

Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations

Cerutti, David S., Trong, Isolde Le, Stenkamp, Ronald E., Lybrand, Terry P.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 5.11 MB

english, 2009

5

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

6

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

7

Use of T cell receptor/HLA-DRB1*04 molecular modeling to predict site-specific interactions for the DR shared epitope associated with rheumatoid arthritis

Julie E. Penzotti, Gerald T. Nepom, Terry P. Lybrand

Journal:

Arthritis & Rheumatism

Year:

1997

Language:

english

File:

PDF, 1.23 MB

english, 1997

8

Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA

Terry Lybrand, Peter Kollman

Journal:

Year:

1985

Language:

english

File:

PDF, 1014 KB

english, 1985

9

Recognition of altered self major histocompatibility complex molecules modulated by specific peptide interactions

Gerald T. Nepom, Dawei Ou, Terry P. Lybrand, Carol Deweese, Mary Ellen Domeier, Jane H. Buckner, Leslie A. Mitchell, Aubrey J. Tingle

Journal:

European Journal of Immunology

Year:

1996

Language:

english

File:

PDF, 527 KB

english, 1996

10

PVM-AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters

Eric Swanson, Terry P. Lybrand

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 966 KB

english, 1995

11

On the absence of stereoselectivity in the catalytic oxidation of alkenes with a surface-bound metalloporphyrin-peptide conjugate

G.Richard Geier III, Terry P. Lybrand, Tomikazu Sasaki

Journal:

Year:

1999

Language:

english

File:

PDF, 732 KB

english, 1999

12

Streptavidin–biotin binding energetics

Patrick S Stayton, Stefanie Freitag, Lisa A Klumb, Ashutosh Chilkoti, Vano Chu, Julie E Penzotti, Richard To, David Hyre, Isolde Le Trong, Terry P Lybrand, Ronald E Stenkamp

Journal:

Biomolecular Engineering

Year:

1999

Language:

english

File:

PDF, 809 KB

english, 1999

13

Molecular Models for Cholecystokinin-A Receptor

Eric S. Dawson, Randel M. Henne, Laurence J. Miller, Terry P. Lybrand

Journal:

Basic & Clinical Pharmacology & Toxicology

Year:

2002

Language:

english

File:

PDF, 83 KB

english, 2002

14

Molecular Basis of Agonist Binding to the Type A Cholecystokinin Receptor

Laurence J. Miller, Terry P. Lybrand

Journal:

Basic & Clinical Pharmacology & Toxicology

Year:

2002

Language:

english

File:

PDF, 122 KB

english, 2002

15

A Molecular Model of Myelin Oligodendrocyte Glycoprotein

Peter Hjelmström, Julie E. Penzotti, Randal M. Henne, Terry P. Lybrand

Journal:

Journal of Neurochemistry

Year:

1998

Language:

english

File:

PDF, 1008 KB

english, 1998

16

Molecular modeling of flexible arm-mediated interactions between bacterial chemoreceptors and their modification enzyme

Usha K. Muppirala, Susan Desensi, Terry P. Lybrand, Gerald L. Hazelbauer, Zhijun Li

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 1022 KB

english, 2009

17

Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus

Terry P. Lybrand, J. Andrew McCammon

Journal:

Journal of Computer-Aided Molecular Design

Year:

1989

Language:

english

File:

PDF, 381 KB

english, 1989

18

Three-dimensional models for integral membrane proteins: Possibilities and pitfalls

Maria Kontoyianni, Terry P. Lybrand

Journal:

Perspectives in Drug Discovery and Design

Year:

1993

Language:

english

File:

PDF, 1.82 MB

english, 1993

19

Characterization of a Novel Reverse-orientation Model for a Peptide/MHC Complex Putatively Associated with Type I Diabetes Mellitus

Carol DeWeese, William W. Kwok, Gerald T. Nepom, Terry P. Lybrand

Journal:

Journal of Molecular Modeling

Year:

1996

Language:

english

File:

PDF, 855 KB

english, 1996

20

Early mechanistic events in biotin dissociation from streptavidin

Hyre, David E., Amon, Lynn M., Penzotti, Julie E., Trong, Isolde Le, Stenkamp, Ronald E., Lybrand, Terry P., Stayton, Patrick S.

Journal:

Natural Structural Biology

Year:

2002

Language:

english

File:

PDF, 2.27 MB

english, 2002

21

An EF-hand in the sodium channel couples intracellular calcium to cardiac excitability

Wingo, Tammy L, Shah, Vikas N, Anderson, Mark E, Lybrand, Terry P, Chazin, Walter J, Balser, Jeffrey R

Journal:

Nature Structural and Molecular Biology

Year:

2004

Language:

english

File:

PDF, 504 KB

english, 2004

22

Diagnostic cross-linking of paired cysteine pairs demonstrates homologous structures for two chemoreceptor domains with low sequence identity

Wing-Cheung Lai, Megan L. Peach, Terry P. Lybrand, Gerald L. Hazelbauer

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 575 KB

english, 2006

23

Modeling the transmembrane domain of bacterial chemoreceptors

Megan L. Peach, Gerald L. Hazelbauer, Terry P. Lybrand

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 3.66 MB

english, 2002

24

A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics

Cerutti, David S., Duke, Robert, Freddolino, Peter L., Fan, Hao, Lybrand, Terry P.

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

25

Chloroplast genome sequencing analysis ofHeterosigma akashiwoCCMP452 (West Atlantic) and NIES293 (West Pacific) strains

Rose Ann Cattolico, Michael A Jacobs, Yang Zhou, Jean Chang, Melinda Duplessis, Terry Lybrand, John McKay, Han Chuan Ong, Elizabeth Sims, Gabrielle Rocap

Journal:

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

26

Conformation and electrostatic potential surfaces of opiates: Relationship to µ- and λ-site binding

Terry P. Lybrand, Peter A. Kollman, Victor C. Yu, Wolfgang Sadée

Journal:

Pharmaceutical Research

Year:

1986

File:

PDF, 3.93 MB

1986

27

Three-Dimensional Models for β-Adrenergic Receptor Complexes with Agonists and Antagonists

Furse, Kristina E., Lybrand, Terry P.

Journal:

Journal of Medicinal Chemistry

Year:

2003

Language:

english

File:

PDF, 490 KB

english, 2003

28

A Structural Model for TCR Recognition of the HLA Class II Shared Epitope Sequence Implicated in Susceptibility to Rheumatoid Arthritis

Julie E. Penzotti, Derek Doherty, Terry P. Lybrand, Gerald T. Nepom

Journal:

Journal of Autoimmunity

Year:

1996

Language:

english

File:

PDF, 188 KB

english, 1996

29

Three-dimensional structure for the β2 adrenergic receptor protein based on computer modeling studies

Keith MaloneyHuss, Terry P. Lybrand

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 2.56 MB

english, 1992

30

Ligand—protein docking and rational drug design

Terry P Lybrand

Journal:

Current Opinion in Structural Biology

Year:

1995

Language:

english

File:

PDF, 524 KB

english, 1995

31

A model for glutathione binding and activation in the fosfomycin resistance protein, FosA

Rachel E. Rigsby, Daniel W. Brown, Eric Dawson, Terry P. Lybrand, Richard N. Armstrong

Journal:

Archives of Biochemistry and Biophysics

Year:

2007

Language:

english

File:

PDF, 558 KB

english, 2007

32

Hydration of chloride and bromide anions: determination of relative free energy by computer simulation

Lybrand, Terry P., Ghosh, Indira, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

1985

Language:

english

File:

PDF, 272 KB

english, 1985

33

Ovalbumin(323−339) Peptide Binds to the Major Histocompatibility Complex Class II I-A d Protein Using Two Functionally Distinct Registers †

McFarland, Benjamin J., Sant, Andrea J., Lybrand, Terry P., Beeson, Craig

Journal:

Year:

1999

Language:

english

File:

PDF, 179 KB

english, 1999

34

Ionic Association in Water: From Atoms to Enzymes

J. ANDREW McCAMMON, OMAR A. KARIM, TERRY P. LYBRAND, CHUNG F. WONG

Journal:

Annals of the New York Academy of Sciences

Year:

1986

Language:

english

File:

PDF, 623 KB

english, 1986

35

Modeling Complex Molecular Interactions Involving Proteins and DNA

PETER A. KOLLMAN, SCOTT WEINER, GEORGE SEIBEL, TERRY LYBRAND, U. CHANDRA SINGH, JAMES CALDWELL, SHASHIDHAR N. RAO

Journal:

Annals of the New York Academy of Sciences

Year:

1986

Language:

english

File:

PDF, 718 KB

english, 1986

36

Computer modeling of actinomycin D interactions with double-helical DNA

Terry P. Lybrand, Steve C. Brown, Steve Creighton, Richard H. Shafer, Peter A. Kollman

Journal:

Journal of Molecular Biology

Year:

1986

Language:

english

File:

PDF, 1.33 MB

english, 1986

37

Site-Directed Spin-Labeling Studies: Structure of the AnkD34-Cdb3 Complex

Kim, Sunghoon, Brandon, Suzanne, Smith, Jarrod A., Edwards, Sarah J., Lybrand, Terry P., Cobb, Charles E., Hustedt, Eric J., Beth, Albert H.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 38 KB

english, 2011

38

Simulation of Nitroxide Electron Paramagnetic Resonance Spectra from Brownian Trajectories and Molecular Dynamics Simulations

DeSensi, Susan C., Rangel, David P., Beth, Albert H., Lybrand, Terry P., Hustedt, Eric J.

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 651 KB

english, 2008

39

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

Le Trong, Isolde, Chu, Vano, Xing, Yi, Lybrand, Terry P., Stayton, Patrick S., Stenkamp, Ronald E.

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2013

Language:

english

File:

PDF, 719 KB

english, 2013

40

Sulindac Derivatives That Activate the Peroxisome Proliferator-activated Receptor γ but Lack Cyclooxygenase Inhibition

Felts, Andrew S., Siegel, Brianna S., Young, Shiu M., Moth, Christopher W., Lybrand, Terry P., Dannenberg, Andrew J., Marnett, Lawrence J., Subbaramaiah, Kotha

Journal:

Journal of Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 985 KB

english, 2008

41

TagDock: An Efficient Rigid Body Docking Algorithm for Oligomeric Protein Complex Model Construction and Experiment Planning

Smith, Jarrod A., Edwards, Sarah J., Moth, Christopher W., Lybrand, Terry P.

Journal:

Year:

2013

Language:

english

File:

PDF, 303 KB

english, 2013

42

Novel Benzodiazepine Photoaffinity Probe Stereoselectively Labels a Site Deep within the Membrane-Spanning Domain of the Cholecystokinin Receptor

Hadac, Elizabeth M., Dawson, Eric S., Darrow, James W., Sugg, Elizabeth E., Lybrand, Terry P., Miller, Laurence J.

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 688 KB

english, 2006

43

Molecular recognition in nonaqueous solvents: sodium ion, potassium ion, and 18-crown-6 in methanol

Mazor, Michael H., McCammon, J. Andrew, Lybrand, Terry P.

Journal:

Journal of the American Chemical Society

Year:

1989

Language:

english

File:

PDF, 233 KB

english, 1989

44

Structure of the CDB3 - ankD34 Complex from Site - Directed Spin - Labeling Studies

Kim, Sunghoon, Hustedt, Eric J., Brandon, Suzanne, Cobb, Charles E., Moth, Christopher W., Parry, Christian S., Lybrand, Terry P., Beth, Albert H.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

45

Calculation of the EPR Spectrum of a Small Nitroxide from Molecular Dynamics Simulations

Kazmier, Kelli N., Lybrand, Terry P., Hustedt, Eric J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 74 KB

english, 2009

46

Modelling the Interactions of Equinatoxin II with Micelles

Weber, Daniel, Yao, Shenggen, Anderluh, Gregor, Lybrand, Terry P., Downton, Matthew T., Wagner, John, Separovic, Frances

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

47

Modelling the Interactions of Equinatoxin II with Micelles

Weber, Daniel, Yao, Shenggen, Anderluh, Gregor, Lybrand, Terry, Downton, Matthew, Wagner, John, Separovic, Frances

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 120 KB

english, 2014

48

Theoretical Calculation of Relative Binding Affinity in Host--Guest Systems

Terry P. Lybrand, J. Andrew McCammon and Georges Wipff

Journal:

Proceedings of the National Academy of Sciences

Year:

1986

Language:

english

File:

PDF, 679 KB

english, 1986

49

A Structural Snapshot of an Intermediate on the Streptavidin-Biotin Dissociation Pathway

Stefanie Freitag, Vano Chu, Julie E. Penzotti, Lisa A. Klumb, Richard To, David Hyre, Isolde Le Trong, Terry P. Lybrand, Ronald E. Stenkamp and Patrick S. Stayton

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 1.36 MB

english, 1999

50

Molecular recognition in nonaqueous solvent. 2. Structural and thermodynamic analysis of cationic selectivity of 18-crown-6 in methanol

Mazor, Michael H., McCammon, J. Andrew, Lybrand, Terry P.

Journal:

Journal of the American Chemical Society

Year:

1990

Language:

english

File:

PDF, 1.07 MB

english, 1990

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