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Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 4/2014, Volume 28, Issue 4, pp. 375 - 400
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 03/2020, Volume 41, Issue 7, pp. 611 - 618
Determination of the ligand‐binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate... 
FEP | REP | perturbation | binding free energy | replica exchange molecular dynamics | BETA 11-40 TRIMER | EXCHANGE MOLECULAR-DYNAMICS | INHIBITORS | EFFICIENT | CHEMISTRY, MULTIDISCIPLINARY | PREDICTION
Journal Article
Journal of Medicinal Chemistry, ISSN 0022-2623, 02/2018, Volume 61, Issue 3, pp. 638 - 649
Underpinning all drug discovery projects is the interaction between a drug and its target, usually a protein. Thus, improved methods for predicting the... 
ABSOLUTE | PROTEIN-LIGAND-BINDING | ACCURATE | CHEMISTRY, MEDICINAL | AFFINITY PREDICTIONS | SIDE-CHAIN | RELATIVE FREE-ENERGY | INHIBITORS | PARAMETERS | MOLECULAR-DYNAMICS SIMULATIONS | BINDING FREE-ENERGIES
Journal Article
Molecular Physics: Special Issue in Honour of Professor Johann Fischer, ISSN 0026-8976, 06/2017, Volume 115, Issue 9-12, pp. 1200 - 1213
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2010, Volume 6, Issue 9, pp. 2559 - 2565
Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations.... 
SPECIFICITY | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | OPTIMIZATION | BIOMOLECULES | POTENTIALS | CHARMM | T4 LYSOZYME | NONPOLAR
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 06/2018, Volume 39, Issue 16, pp. 986 - 992
Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by... 
free energy perturbation | protein kinases | homoarginine | unnatural amino acid modeling | cAMP‐dependent kinase | PKA | cAMP-dependent kinase | CATALYTIC SUBUNIT | MOLECULAR-DYNAMICS | PHOSPHORYLATION REACTION | SPECIFICITY | MECHANISM | QM/MM | CHEMISTRY, MULTIDISCIPLINARY | SUBSTRATE | INHIBITORS | Tyrosine | Molecular dynamics | Peptides | Arginine | Protein kinases | Analysis
Journal Article
ChemMedChem, ISSN 1860-7179, 01/2016, Volume 11, Issue 2, pp. 217 - 233
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 2019, Volume 59, Issue 6, pp. 2729 - 2740
Journal Article
Chemical Biology & Drug Design, ISSN 1747-0277, 10/2015, Volume 86, Issue 4, pp. 546 - 558
The binding mechanism of AC1NX476 to HIV‐1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free... 
docking | binding cavity | AC1NX476 | binding free energy | ritonavir | free energy perturbation method | darunavir | HIV‐1 protease | HIV-1 protease | HIV Protease - genetics | Models, Molecular | HIV-1 - enzymology | HIV Protease - chemistry | Mutation | HIV-1 - genetics | Darunavir - chemistry | Ritonavir - chemistry | Genetic aspects | HIV (Viruses) | Proteases | Analysis | Methods
Journal Article
The Journal of Physical Chemistry C, ISSN 1932-7447, 03/2017, Volume 121, Issue 12, pp. 6868 - 6873
The solid–vapor interfacial free energy γ sv plays an important role in a number of physical phenomena, such as adsorption, wetting, and adhesion. We propose a... 
COEXISTENCE | EQUATION-OF-STATE | SURFACE FREE-ENERGIES | MATERIALS SCIENCE, MULTIDISCIPLINARY | CRYSTAL FLUID INTERFACE | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | LENNARD-JONES SYSTEM | DENSITY-FUNCTIONAL THEORY | SIMULATION | LIQUIDS
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 08/2012, Volume 8, Issue 8, pp. 2606 - 2616
As computational power inexorably continues to grow, harnessing the capabilities of novel processing units and architectures, free-energy calculations are... 
SOLVATION FREE-ENERGIES | LIGAND-BINDING | PROTEIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | THERMODYNAMIC DECOMPOSITION | CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | FORCE-FIELD | MOLECULAR-DYNAMICS SIMULATIONS | BINDING FREE-ENERGIES | HYDRATION | ACCURACY
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 10/2009, Volume 5, Issue 10, pp. 2583 - 2588
Distributed Replica (REPDSTR) is a powerful parallelization technique enabling simulations of a group of replicas in a parallel/parallel fashion, where each... 
CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | CHARMM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | SAMPLING | THERMODYNAMICS | INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY | REPLICAS | CONVERGENCE | SIMULATION | HYDRATION | FREE ENERGY
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 07/2019, Volume 15, Issue 7, pp. 3941 - 3948
Journal Article
Journal of Molecular Biology, ISSN 0022-2836, 04/2017, Volume 429, Issue 7, pp. 930 - 947
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 03/2013, Volume 138, Issue 11, p. 114111
In this work we propose a multidimensional free energy perturbation scheme that allows the evaluation of the free energy difference between a state sampled... 
ENSEMBLE | REINSERTION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | PARTICLE DELETION SCHEME | SWITCH | SIMULATION | ENTROPY | Thermodynamics | Temperature | Entropy | Models, Chemical | Pressure | Computer Simulation | Construction | Simulation | Isotherms | Perturbation | Thermodynamic properties | Free energy | Importance sampling | State variable
Journal Article