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a r t i c l e i n f o a b s t r a c t The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific(More)
NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and(More)
The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short(More)
The paper describes an efficient communication support for the global address space programming model on the IBM SP, a commercial example of the SMP (symmetric multi-processor) clusters. Our approach integrates shared memory with active messages, threads and remote memory copy between nodes. The shared memory operations offer substantial performance(More)
Even if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are significant. Molecular docking using such a receptor structure may thus fail to recognize a ligand to which the receptor can bind with reasonable affinity. Here, we examine one way to alleviate this(More)
  • S Istrail, P Pevzner, M Waterman, Editorial Board, A Apostolico, S Brunak +131 others
  • 2008
(Brasília, Distrito Federal). The change from workshop to symposium reflects the increasing quality and interest behind this meeting. For BSB 2008, we had 41 submissions: 32 full papers and 9 extended abstracts , submitted to two tracks: the main track on Computational Biology and Bioinformatics, and the track Applications of Agent Technologies and(More)
Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the(More)
Two molecular dynamics simulations were performed for a modeled complex of mouse acetylcholinesterase liganded with huperzine A (HupA). Analysis of these simulations shows that HupA shifts in the active site toward Tyr 337 and Phe 338, and that several residues in the active site area reach out to make hydrogen bonds with the inhibitor. Rapid fluctuations(More)