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Process Biochemistry, ISSN 1359-5113, 07/2019
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 09/2012, Volume 8, Issue 9, pp. 3257 - 3273
While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the... 
REFINEMENT | FOLDING SIMULATIONS | EXPLICIT WATER | BETA-HAIRPIN | NMR-SPECTROSCOPY | RESOLUTION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SECONDARY STRUCTURE | COUPLINGS | MODEL | MOLECULAR-DYNAMICS SIMULATIONS
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2014, Volume 10, Issue 11, pp. 5113 - 5124
Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific proteinprotein interactions being too strong, and unfolded or... 
HYDRATION FREE-ENERGIES | SOLVATION FREE-ENERGIES | FOLDING SIMULATIONS | BETA-HAIRPIN | N-15 NMR RELAXATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | POLARIZABLE FORCE-FIELDS | CHEMISTRY, PHYSICAL | UNFOLDED PROTEINS | SIDE-CHAIN ANALOGS | MOLECULAR-DYNAMICS SIMULATIONS | VILLIN HEADPIECE SUBDOMAIN
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 12/2013, Volume 9, Issue 12, pp. 5430 - 5449
Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and... 
INITIO QUANTUM-CHEMISTRY | COLD-SHOCK PROTEIN | FLUCTUATING CHARGE | LIGAND-BINDING | N-15 NMR RELAXATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE METHOD | POTENTIAL FUNCTIONS | PANCREATIC TRYPSIN-INHIBITOR | MOLECULAR-DYNAMICS SIMULATIONS | BETA-HAIRPIN FORMATION
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 05/2011, Volume 134, Issue 17, pp. 174105 - 174105-23
Journal Article
Computer Physics Communications, ISSN 0010-4655, 2009, Volume 180, Issue 10, pp. 1961 - 1972
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most... 
Proteins | Molecular dynamics | Metadynamics | Umbrella sampling | Free energy | BETA-HAIRPIN | MECHANISM | ALGORITHMS | SIMULATION | PHYSICS, MATHEMATICAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | REPLICA-EXCHANGE | FORCE-FIELD | SYSTEMS | EFFICIENT | Chemical properties | Universities and colleges
Journal Article
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 2012, Volume 8, Issue 8, pp. 2725 - 2740
We have compared molecular dynamics (MD) simulations of a beta-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using... 
RECOGNITION MODEL | EXPLICIT WATER | WW DOMAIN | BETA-HAIRPIN | FREE-ENERGY LANDSCAPE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PROTEIN-FOLDING SIMULATIONS | INTRINSICALLY UNSTRUCTURED PROTEINS | HELIX-COIL TRANSITION | POTENTIAL FUNCTIONS | VILLIN HEADPIECE
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2004, Volume 108, Issue 21, pp. 6571 - 6581
A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics... 
TOPOLOGY | BETA-HAIRPIN | MARKOV-CHAINS | LANDSCAPE | LUMPABILITY | MASTER EQUATION | CHEMISTRY, PHYSICAL | BLUE GENE | TRP-CAGE | FREE-ENERGY | SURFACES
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 12/2018, Volume 122, Issue 49, pp. 11390 - 11399
When proteins bind to interfaces, the resulting changes in protein structure can lead to loss of protein function. We investigate the mechanism by which... 
TWEEN 80 | BETA-HAIRPIN | FREE-ENERGY LANDSCAPES | RECOMBINANT | STABILITY | AGITATION | CHEMISTRY, PHYSICAL | MOLECULAR-DYNAMICS SIMULATIONS | BINDING | AGGREGATION | WATER
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 08/2011, Volume 115, Issue 30, pp. 9431 - 9438
A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for... 
EXPLICIT WATER | BETA-HAIRPIN | PROTEIN | CHEMISTRY, PHYSICAL | SYSTEMS | SIMULATIONS | ENERGY LANDSCAPE | Thermodynamics | Temperature | Proteins - chemistry | Protein Structure, Secondary | Protein Folding | Water - chemistry | Temperature measurements | Water chemistry | Analysis | Exchange | Proteins | Rest | Tempering | Central processing units | Computing time | Sampling | Folding | Index Medicus
Journal Article
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, 06/2003, Volume 100, Issue 13, pp. 7587 - 7592
Replica-exchange molecular dynamics simulations in implicit solvent have been carried out to study the folding thermodynamics of a designed 20-residue peptide,... 
MOLECULAR-DYNAMICS | EXPLICIT WATER | NMR | BETA-HAIRPIN | PROTEIN | FREE-ENERGY LANDSCAPE | MULTIDISCIPLINARY SCIENCES | BIOLOGICAL MOLECULES | FORCE-FIELD | SOLVENT | PEPTIDE
Journal Article
BIOPHYSICAL JOURNAL, ISSN 0006-3495, 08/2014, Volume 107, Issue 4, pp. 991 - 997
Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly... 
POLARIZABLE FORCE-FIELD | BETA-HAIRPIN | ALPHA-HELIX | BIOPHYSICS | COIL TRANSITION | ALANINE-BASED PEPTIDES | PROTEIN-FOLDING SIMULATIONS | TRP-CAGE | HUMAN LYSOZYME | MOLECULAR-DYNAMICS SIMULATIONS | CHARMM
Journal Article
JOURNAL OF ORGANIC CHEMISTRY, ISSN 0022-3263, 11/2017, Volume 82, Issue 21, pp. 11326 - 11336
Diarylmethylamido bis(phenols) have been subjected to peptide-catalyzed, enantioselective bromination reactions. Desymmetrization of compounds in this class... 
LEWIS-BASE CATALYSIS | ENANTIOSELECTIVE SYNTHESIS | CHIRAL DIENE LIGANDS | KINETIC RESOLUTION | CHEMISTRY, ORGANIC | N-TOSYLARYLIMINES | ASYMMETRIC ARYLATION | BETA-HAIRPIN FORMATION | DERIVATIVES | C-H BONDS | ARYLBORONIC ACIDS
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2008, Volume 112, Issue 19, pp. 6057 - 6069
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 02/2016, Volume 138, Issue 5, pp. 1543 - 1550
The design of folded miniature proteins is predicated on establishing noncovalent interactions that direct the self-assembly of discrete thermostable tertiary... 
DESIGNED BETA-HAIRPIN | WSXWS MOTIF | CHAIN | COMPLEX | CIRCULAR-DICHROISM | RECOGNITION | CRYSTAL-STRUCTURE | BINDING | CHEMISTRY, MULTIDISCIPLINARY | CYTOKINE RECEPTORS | REVEALS | Sulfur compounds | Cations | Chemical properties | Arginine | Analysis
Journal Article
NUCLEIC ACIDS RESEARCH, ISSN 0305-1048, 05/2019, Volume 47, Issue 8, pp. 4136 - 4152
The UvrA(2) dimer finds lesions in DNA and initiates nucleotide excision repair. Each UvrA monomer contains two essential ATPase sites: proximal (P) and distal... 
BINDING CASSETTE TRANSPORTER | BETA-HAIRPIN | RECOGNITION | (A)BC EXCINUCLEASE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | DNA-DAMAGE | ESCHERICHIA-COLI UVRA | ABC TRANSPORTERS | INCISION | PROTEINS
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 02/2019, Volume 47, Issue 3, pp. 1523 - 1531
Abstract The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex... 
DESIGN | MIMICRY | PROTEIN | BETA-HAIRPIN PEPTIDOMIMETICS | NONCODING RNAS | SMALL-MOLECULE INHIBITORS | BIOCHEMISTRY & MOLECULAR BIOLOGY | CONFORMATION | BASE TRIPLE | BINDING | DISCOVERY | RNA and RNA-protein complexes
Journal Article
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