CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and modelbuilding capabilities. The CHARMM program is applicable to problems involving a much broader class of manyparticle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanicalmolecular mechanical force fields, to allatom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. Coauthor of the article and coauthor of the program package CHARRM (M. Hodoscek) would like to stress that the program CHARRM was one of the important reasons for Nobel prize awarded to Martin Karplus in 2013.
COBISS.SI-ID: 4194586
This paper reports the application of the adaptive resolution scheme (AdResS) for simulating aqueous salt solutions. The concurrent multiscale method AdResS allows for a dynamical change of molecular resolution by coupling atomistic and coarsegrained models of liquids. To this end, we have developed coarsegrained models of salt to be used with standard atomistic force fields and derive thermodynamic forces to ensure the thermodynamic equilibrium distribution of all molecular species across the simulation box.
COBISS.SI-ID: 5301530
Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4,5 bithiazols inhibitors of gyrase B with a low micromolar inhibitory activity, by implementing a twostep structurebased design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques: Differential Scanning Fluorimetry (DSF), Surface Plasmon Resonance (SPR) and microscale thermophoresis (MST). The binding mode of the potent inhibitor was revealed by Xray crystallography,confirming our initial in silico binding model.
COBISS.SI-ID: 4999450
Using molecular dynamics simulations in conjunction with homedeveloped Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures.
COBISS.SI-ID: 5014554
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the molecular scale HE has an entropic origin. It is believed that hydrophobic particles induce order in the surrounding water by reducing the volume of configuration space available for hydrogen bonding. Here we show with computer simulation results that this traditional picture, based on average structural features of hydration water, configurational properties of single water molecules, and up to pairwise correlations, is not correct. Analyzing collective fluctuations in water clusters we are able to provide a fundamentally new picture of HE based on pronounced many-body correlations affecting the switching of hydrogen bonds (HBs) between molecules. These correlations emerge as a nonlocal compensation of reduced fluctuations of local electrostatic fields in the presence of an apolar solute. We propose an alternative view which may also be formulated as a maximization principle: The electrostatic noise acting on water molecules is maximized under the constraint that each water molecule on average maintains as many HBs as possible. In the presence of the solute the maximized electrostatic noise is a result of nonlocal fluctuations in the labile HB network giving rise to strong correlations among at least up to four water molecules.
COBISS.SI-ID: 5094426