Author
Malcolm E. Davis
Other affiliations: University of Houston
Bio: Malcolm E. Davis is an academic researcher from Bristol-Myers Squibb. The author has contributed to research in topics: Protein ligand & Poisson–Boltzmann equation. The author has an hindex of 22, co-authored 29 publications receiving 3471 citations. Previous affiliations of Malcolm E. Davis include University of Houston.
Papers
More filters
••
TL;DR: A general-purpose Brownian dynamics program that has been developed at the University of Houston is described in this paper, where the diffusion of flexible chains is modeled by the finite difference solutions of the linearized Poisson-Boltzmann equation.
908 citations
••
680 citations
••
TL;DR: In this article, an accurate method for computing the forces acting in a system governed by the Poisson-Boltzmann equation (PBE) is presented. But the method is not suitable for the case of a high dielectric aqueous solvent on the solute surface.
Abstract: Numerical solutions of the Poisson-Boltzmann equation (PBE) have found wide application in the computation of electrostatic energies of hydrated molecules, including biological macromolecules. However, solving the PBE for electrostatic forces has proved more difficult, largely because of the challenge of computing the pressures exerted by a high dielectric aqueous solvent on the solute surface. This paper describes an accurate method for computing these forces. We begin by presenting a novel derivation of the forces acting in a system governed by the PBE
339 citations
••
TL;DR: The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
Abstract: Comparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite-difference form of the linearized Poisson-Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
198 citations
••
TL;DR: In this paper, the Particle-Particle Particle Mesh (PPPM) and Ewald methods for calculating electrostatic interactions in periodic molecular systems were compared. But the Ewald method requires significantly less computational effort than the PPPM and scales almost linearly with system size.
Abstract: We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods for calculating electrostatic interactions in periodic molecular systems. A brief comparison of the theories shows that the methods are very similar differing mainly in the technique which is used to perform the “k-space” or mesh calculation. Because the PPPM utilizes the highly efficient numerical Fast Fourier Transform (FFT) method it requires significantly less computational effort than the Ewald method and scales almost linearly with system size.
183 citations
Cited by
More filters
01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.
29,323 citations
••
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072
13,286 citations
••
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.
8,377 citations
••
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
7,672 citations
••
TL;DR: The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.
Abstract: Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.
6,918 citations