T. Lybrand

发表

Computer modeling of actinomycin D interactions with double-helical DNA.

P. Kollman, T. Lybrand, S. Brown, 1986, Journal of molecular biology.

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

Peter L. Freddolino, T. Lybrand, D. Cerutti, 2008, Journal of chemical theory and computation.

Ligand-protein docking and rational drug design.

T. Lybrand, 1995, Current Opinion in Structural Biology.

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

P. Kollman, T. Lybrand, 1985 .

Three-dimensional models for beta-adrenergic receptor complexes with agonists and antagonists.

Terry P Lybrand, T. Lybrand, Kristina E Furse, 2003, Journal of medicinal chemistry.

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

T. Lybrand, G. L. Hazelbauer, Zhijun Li, 2009, Protein science : a publication of the Protein Society.

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

T. Lybrand, J. Mccammon, M. Mazor, 1989 .

Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

T. Lybrand, R. A. Cattolico, Jean Chang, 2008, BMC Genomics.

Enhanced Dispersion and Polarization Interactions Achieved through Dithiophosphate Group Incorporation Yield a Dramatic Binding Affinity Increase for an RNA Aptamer-Thrombin Complex.

T. Lybrand, M. Egli, 2019, Journal of the American Chemical Society.

Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

T. Lybrand, M. Egli, J. Smith, 2019, Crystals.

Supercomputer Chemistry Structure, Dynamics, and Biochemical Applications

T. Lybrand, D. Truhlar, J. Almlöf, 1990 .

PAP : a protein analysis package.

T. Lybrand, W. B. Gleason, T. Callahan, 1990 .

Polymorphic amino acid variations in HLA-DQ are associated with systematic physical property changes and occurrence of IDDM. Members of the Swedish Childhood Diabetes Study.

T. Lybrand, Å. Lernmark, I. Kockum, 1995 .

Cryo neutron crystallography demonstrates influence of RNA 2′-OH orientation on conformation, sugar pucker and water structure

T. Lybrand, M. Egli, L. Coates, 2022, Nucleic acids research.

Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA.

P. Kollman, T. Lybrand, D. Jerina, 1989, Carcinogenesis.

Molecular Modeling of the Interactions between Carborane-Containing Analogs of Indomethacin and Cyclooxygenase-2

T. Lybrand, E. Hey‐Hawkins, M. Sárosi, 2017, J. Chem. Inf. Model..

Structural Determinants of Arylacetic Acid Nonsteroidal Anti-Inflammatory Drugs Necessary for Binding and Activation of the Prostaglandin D2 Receptor CRTH2

T. Lybrand, L. Marnett, R. Breyer, 2005, Molecular Pharmacology.

Structural determinants of arylacetic acid NSAIDs necessary for binding and activation of the PGD 2 receptor CRTH2

T. Lybrand, L. Marnett, R. Breyer, 2004 .

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

T. Lybrand, J. Penzotti, G. Nepom, 1997, Arthritis and rheumatism.

Spatial Approximation between Two Residues in the Mid-region of Secretin and the Amino Terminus of Its Receptor

T. Lybrand, Zhijun Li, Mengwei Zang, 2003, Journal of Biological Chemistry.

Active site of bee venom phospholipase A2: the role of histidine-34, aspartate-64 and tyrosine-87.

T. Lybrand, M. Gelb, J. Penzotti, 1996, Biochemistry.

Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States

L. Zhao, T. Lybrand, D. Geraghty, 2022, JAMA network open.

A structural model for TCR recognition of the HLA class II shared epitope sequence implicated in susceptibility to rheumatoid arthritis.

T. Lybrand, J. Penzotti, D. Doherty, 1996, Journal of autoimmunity.

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

T. Lybrand, Tomikazu Sasaki, G. Geier, 1999 .

Rapidly identifying new coronavirus mutations of potential concern in the Omicron variant using an unsupervised learning strategy

L. Zhao, T. Lybrand, D. Geraghty, 2022, Scientific Reports.

A peptide agonist acts by occupation of a monomeric G protein-coupled receptor: dual sites of covalent attachment to domains near TM1 and TM7 of the same molecule make biologically significant domain-swapped dimerization unlikely.

T. Lybrand, L. Miller, E. Hadac, 1999, Journal of medicinal chemistry.

Variants in nucleocapsid protein and endoRNase are found to associate with severe COVID-19 in a case-control study in Washington State, USA

L. Zhao, T. Lybrand, J. Schiffer, 2021 .

Analysis of critical residues of HLA-DQ6 molecules in insulin-dependent diabetes mellitus.

T. Lybrand, Å. Lernmark, I. Kockum, 1997, Tissue antigens.

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

T. Lybrand, G. Nepom, W. Kwok, 1996 .

Transmembrane segment peptides can disrupt cholecystokinin receptor oligomerization without affecting receptor function.

T. Lybrand, L. Miller, Zhi-jie Cheng, 2006, Biochemistry.

Novel benzodiazepine photoaffinity probe stereoselectively labels a site deep within the membrane-spanning domain of the cholecystokinin receptor.

T. Lybrand, L. Miller, E. Hadac, 2006, Journal of medicinal chemistry.

Molecular dynamics simulations of arachidonic acid-derived pentadienyl radical intermediate complexes with COX-1 and COX-2: insights into oxygenation regio- and stereoselectivity.

T. Lybrand, A. Brash, D. Pratt, 2006, Biochemistry.

Targeted Molecular Dynamics Simulations Suggest Direct Ligand Competition as a Plausible Efflux Inhibition Mechanism in the Multidrug Resistance Pump AcrB

T. Lybrand, K. Machado, P. A. D. da Silva, 2018, bioRxiv.

Moleular models for cholecystokinin-A receptor.

T. Lybrand, L. Miller, E. Dawson, 2002, Pharmacology & toxicology.

Polymorphic Amino Acid Variations in HLA-DQ Are Associated With Systematic Physical Property Changes and Occurrence of IDDM

T. Lybrand, I. Kockum, G. Dahlquist, 1995, Diabetes.

Theoretical calculation of relative binding affinity in host-guest systems.

J A McCammon, T. Lybrand, J. Mccammon, 1986, Proceedings of the National Academy of Sciences of the United States of America.

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

T. Lybrand, R. Gomer, A. Sood, 2016, Nucleic acids research.

Modeling Complex Molecular Interactions Involving Proteins and DNA a

U. Singh, P. Kollman, S. Weiner, 1986, Annals of the New York Academy of Sciences.

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.

T. Lybrand, M. Manoharan, M. Egli, 2020, Biochemistry.

Molecular Modeling of Eluted Peptides from DQ6 Molecules (DQB1*0602 and DQB1*0604) Negatively and Positively Associated with Type 1 Diabetes

T. Lybrand, H. Rammensee, S. Stevanović, 2002, Annals of the New York Academy of Sciences.

PDFlib PLOP: PDF Linearization, Optimization, Protection Page inserted by evaluation version

T. Lybrand, H. Rammensee, S. Stevanović, 2002 .

Structural basis of specificity and degeneracy of T cell recognition: pluriallelic restriction of T cell responses to a peptide antigen involves both specific and promiscuous interactions between the T cell receptor, peptide, and HLA-DR.

T. Lybrand, J. Penzotti, D. Doherty, 1998, Journal of immunology.

Structural differences between HLA-DQ molecules associated with myasthenia gravis characterized by molecular modeling

T. Lybrand, J. Penzotti, C. Sanjeevi, 1998, Journal of Neuroimmunology.

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

T. Lybrand, G. Nepom, J. Buckner, 1996, European journal of immunology.

DR4 subtypes and their molecular properties in a population-based study of Swedish childhood diabetes.

T. Lybrand, Å. Lernmark, I. Kockum, 1996, Tissue antigens.

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

Andrew S. Felts, T. Lybrand, L. Marnett, 2008, Journal of medicinal chemistry.

Analysis of antibody markers, DRB1, DRB5, DQA1 and DQB1 genes and modeling of DR2 molecules in DR2-positive patients with insulin-dependent diabetes mellitus.

T. Lybrand, Å. Lernmark, W. Hagopian, 1994, Tissue antigens.

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

T. Lybrand, M. Kontoyianni, 1993 .

The KAG motif of HLA-DRB1 (β71, β74, β86) predicts seroconversion and development of type 1 diabetes

L. Zhao, T. Lybrand, Å. Lernmark, 2021, EBioMedicine.

Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation.

T. Lybrand, S. Yao, G. Anderluh, 2015, Biophysical journal.

Ovalbumin(323-339) peptide binds to the major histocompatibility complex class II I-A(d) protein using two functionally distinct registers.

T. Lybrand, A. Sant, C. Beeson, 1999, Biochemistry.

Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods

T. Lybrand, 2007 .

Stereoselective binding of indomethacin ethanolamide derivatives to cyclooxygenase-1.

T. Lybrand, L. Marnett, C. Moth, 2005, Journal of medicinal chemistry.

Interaction among four residues distributed through the secretin pharmacophore and a focused region of the secretin receptor amino terminus.

T. Lybrand, Zhijun Li, Mengwei Zang, 2002, Molecular endocrinology.

Protein Stability and Function

Terry P. Lybrand, J. Andrew McCammon, Chung F. Wong, 1989 .

Identification of Determinants of Ligand Binding Affinity and Selectivity in the Prostaglandin D2 Receptor CRTH2*

T. Lybrand, R. Breyer, A. Hata, 2005, Journal of Biological Chemistry.

Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020—March 2021) Using a Statistical Learning Strategy

Lindsay N. Carpp, L. Zhao, T. Lybrand, 2021, Viruses.

Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 – 2021/03) Using a Statistical Learning Strategy

Lindsay N. Carpp, L. Zhao, T. Lybrand, 2021, bioRxiv.

Determination of Structural Models of the Complex between the Cytoplasmic Domain of Erythrocyte Band 3 and Ankyrin-R Repeats 13–24*

Terry P. Lybrand, Eric J. Hustedt, Albert H. Beth, 2011, The Journal of Biological Chemistry.

Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk

L. Zhao, T. Lybrand, D. Geraghty, 2022, Scientific Reports.

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

Terry P. Lybrand, Peter A. Kollman, Piotr Cieplak, 1987 .

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

Michael H. Mazor, T. Lybrand, J. Mccammon, 1990 .

Protein-Ligand Interactions

Terry P. Lybrand, T. Lybrand, 2002 .

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

Terry P. Lybrand, J. Andrew McCammon, Indira Ghosh, 1985 .

Refinement of the conformation of a critical region of charge-charge interaction between cholecystokinin and its receptor.

T. Lybrand, L. Miller, D. Pinon, 2002, Molecular pharmacology.

Direct Identification of a Distinct Site of Interaction between the Carboxyl-terminal Residue of Cholecystokinin and the Type A Cholecystokinin Receptor Using Photoaffinity Labeling*

T. Lybrand, L. Miller, Z. Ji, 1997, The Journal of Biological Chemistry.

Spatial Approximation between the Amino Terminus of a Peptide Agonist and the Top of the Sixth Transmembrane Segment of the Secretin Receptor*

T. Lybrand, Zhijun Li, L. Miller, 2004, Journal of Biological Chemistry.

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

L. Zhao, T. Lybrand, D. Geraghty, 2023, JAMA network open.

A new water potential including polarization: Application to gas‐phase, liquid, and crystal properties of water

Terry P. Lybrand, Peter A. Kollman, Piotr Cieplak, 1990 .

Supercomputer Chemistry At the University of Minnesota

Klavs F. Jensen, Donald G. Truhlar, Matthew Tirrell, 1988 .

Spatial approximation between a photolabile residue in position 13 of secretin and the amino terminus of the secretin receptor.

T. Lybrand, Zhijun Li, Mengwei Zang, 2003, Molecular pharmacology.

Molecular dynamics simulations of arachidonic acid complexes with COX-1 and COX-2: insights into equilibrium behavior.

Terry P Lybrand, Derek A Pratt, T. Lybrand, 2006, Biochemistry.

Refinement of the Structure of the Ligand-occupied Cholecystokinin Receptor Using a Photolabile Amino-terminal Probe*

T. Lybrand, L. Miller, E. Hadac, 2001, The Journal of Biological Chemistry.

Direct Identification of a Second Distinct Site of Contact between Cholecystokinin and Its Receptor*

T. Lybrand, L. Miller, E. Hadac, 1998, The Journal of Biological Chemistry.

Conservative Secondary Shell Substitution In Cyclooxygenase-2 Reduces Inhibition by Indomethacin Amides and Esters via Altered Enzyme Dynamics

Anna L. Blobaum, T. Lybrand, L. Marnett, 2015, Biochemistry.

Streptavidin and its biotin complex at atomic resolution.

Zhizhi Wang, Terry P Lybrand, T. Lybrand, 2011, Acta crystallographica. Section D, Biological crystallography.

Streptavidin-biotin binding energetics.

T. Lybrand, J. Penzotti, A. Chilkoti, 1999, Biomolecular engineering.

A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway.

T. Lybrand, J. Penzotti, D. Hyre, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Molecular basis of agonist binding to the type A cholecystokinin receptor.

T. Lybrand, L. Miller, 2002, Pharmacology & toxicology.

Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies.

T P Lybrand, K MaloneyHuss, T. Lybrand, 1992, Journal of molecular biology.

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

T. Lybrand, D. Cerutti, P. Stayton, 2010, Biochemistry.

Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

Terry P Lybrand, David S Cerutti, Robert E Duke, 2009, Journal of chemical theory and computation.

Analysis of the pharmacological properties of clozapine analogues using molecular electrostatic potential surfaces

P. Kollman, T. Lybrand, H. Weber, 1986 .

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

Rachel E Rigsby, T. Lybrand, R. Armstrong, 2007, Archives of biochemistry and biophysics.

Measurement of intermolecular distances for the natural agonist Peptide docked at the cholecystokinin receptor expressed in situ using fluorescence resonance energy transfer.

T. Lybrand, L. Miller, K. Harikumar, 2004, Molecular pharmacology.

Erratum: Spatial approximation between a photolabile residue in position 13 of secretin and the amino terminus of the secretin receptor (Molecular Pharmacology (2003) 63 (993-1001))

T. Lybrand, Zhijun Li, Mengwei Zang, 2003 .

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

T. Lybrand, J. Balser, W. Chazin, 2004, Nature Structural &Molecular Biology.

Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

Cody R. Goodwin, T. Lybrand, J. McLean, 2014, The journal of physical chemistry. B.

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

P. Kollman, T. Lybrand, 1985, Biopolymers.

A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex.

U. Singh, P. Kollman, D. Case, 1989, Journal of biomolecular structure & dynamics.

Molecular Dynamics Simulation of Cyclooxygenase-2 Complexes with Indomethacin closo-Carborane Analogs

Terry P Lybrand, Menyhárt-Botond Sárosi, T. Lybrand, 2018, J. Chem. Inf. Model..

Ionic Association in Water: From Atoms to Enzymes a

Chung F. Wong, J A McCammon, T. Lybrand, 1986, Annals of the New York Academy of Sciences.

Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.

T. Lybrand, D. Cerutti, R. Stenkamp, 2008, Biochemistry.

TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning.

Jarrod A Smith, Sarah J Edwards, Christopher W Moth, 2013, Biochemistry.

Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.

Terry P Lybrand, David S Cerutti, T. Lybrand, 2009, The journal of physical chemistry. B.

Automated Structure Refinement for a Protein Heterodimer Complex Using Limited EPR Spectroscopic Data and a Rigid-Body Docking Algorithm: A Three-Dimensional Model for an Ankyrin-CDB3 Complex

T. Lybrand, Sunghoon Kim, A. Beth, 2014, The journal of physical chemistry. B.

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

Terry P. Lybrand, James Andrew McCammon, T. Lybrand, 1989, J. Comput. Aided Mol. Des..

MD Display: an interactive graphics program for visualization of molecular dynamics trajectories.

T P Lybrand, T J Callahan, E Swanson, 1996, Journal of molecular graphics.

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

Megan L. Peach, T. Lybrand, G. L. Hazelbauer, 2006, Protein science : a publication of the Protein Society.

Modeling the transmembrane domain of bacterial chemoreceptors

Terry P Lybrand, Megan L. Peach, Megan L Peach, 2002, Protein science : a publication of the Protein Society.

Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.

Terry P Lybrand, Albert H Beth, Eric J Hustedt, 2008, Biophysical journal.

A Comparison of Perturbation Methods and Poisson-Boltzmann Electrostatics Calculations for Estimation of Relative Solvation Free Energies

Terry P. Lybrand, Todd J. A. Ewing, T. Lybrand, 1994 .

Molecular Dynamics of Coat Proteins of the Human Rhinovirus

T. Lybrand, B. Pettitt, W. Lau, 1988 .