Robert J. Petrella

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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 a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals,(More)
BACKGROUND Homology modeling is an important technique for making use of the rapidly increasing number of protein sequences in the absence of structural information. The major problems in such modeling, once the alignment has been made, concern the positions of loops and the orientations of sidechains. Although progress has been made in recent years for(More)
Non-rotameric ("off-rotamer") conformations are commonly observed for the side-chains of protein crystal structures. This study examines whether such conformations are real or artifactual by comparing the energetics of on and off-rotamer side-chain conformations calculated with the CHARMM energy function. Energy-based predictions of side-chain orientation(More)
Processivity factors tether the catalytic subunits of DNA polymerases to DNA so that continuous synthesis of long DNA strands is possible. The human cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer intermediate in structure between monomeric herpes simplex virus UL42, which binds DNA directly via a basic surface, and the trimeric(More)
A novel molecular structure prediction method, the Z Method, is described. It provides a versatile platform for the development and use of systematic, grid-based conformational search protocols, in which statistical information (i.e., rotamers) can also be included. The Z Method generates trial structures by applying many changes of the same type to a(More)
Generation of the list of near-neighbor pairs of atoms not bonded to each other is a key feature of many programs for calculating the energy and energy derivatives for large molecules. Because this step can take a significant amount of CPU time, more efficient nonbonded list generation can speed up the energy calculations. In this article, a novel nonbonded(More)
Although most side-chain torsion angles correspond to low-energy rotameric positions, deviations occur with significant frequency. One striking example arises in Trp residues, which have an important role in stabilizing protein structures because of their size and mixed hydrophobic/hydrophilic character. Ten percent of Trp side-chains have unexplained(More)
Peripheral blood leukocytes from ARC and AIDS patients were examined before and after phytohemagglutinin (PHA) stimulation by dual color flow cytometry and monoclonal antibodies which identify developmental and activational stages of T lymphocytes, B cells and monocytes. There was a persistent elevation in the total number of circulating Ia+ lymphocytes(More)
A rapid method for the calculation of the electrostatic energy of a system without a cutoff is described in which the computational time grows linearly with the number of particles or charges. The inverse of the distance is approximated as a polynomial, which is then transformed into a function whose terms involve individual particles, instead of particle(More)