Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must...Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must be able to access computing resources. One way to provide such resources is through High-Performance Computing (HPC) centers. Many academic research institutions offer their own HPC Centers but struggle to make the computing resources easily accessible and user-friendly. Here we present SHABU, a RESTful Web API framework that enables S & E communities to access resources from Boston University’s Shared Computing Center (SCC). The SHABU requirements are derived from the use cases described in this work.展开更多
An inspection of the φ-ψ angle distribution strongly suggests that protein folding is highly constrained. A number of researchers have even suggested that a relatively small set of discrete φ-ψ regions might be su...An inspection of the φ-ψ angle distribution strongly suggests that protein folding is highly constrained. A number of researchers have even suggested that a relatively small set of discrete φ-ψ regions might be sufficient to describe most protein conformation. The total of 541 tight turns from 101 non-identical proteins were extracted form Brookhaven DataBank. The dihedral values of tight turns were scattered into the seven regions on the Ramachandran plot. These seven regions were called A1, A2, B1, B2, B22, T1 and T2. A1 and A2 are the traditional a-helix regions, B1, B2 and B22 the β-strand regions, Tl and T2 the β-turn regions. The A2 and T2 regions were not defined as 'discrete' or single points but rather as one dimensional extended states. Based on the geometry of the two central residues of the tight turns, the new classification of β-turn was defined. This classification of the majority of β-turns fell into only six of the possible forty nine region combinations and were identifiable with the traditional nomenclature of Venkat-achalam(1), but much simpler.The function of β-turn in the conformation of proteins was studied. The hydrophobicity for different type turns was discussed. It shows that β-turns have very strong hydrophilic property, so they are usually situated at the folding protein surface. The features of β-turn and its amino acid distribution in this 541 β-turn group and different type β-turn were given.展开更多
文摘Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must be able to access computing resources. One way to provide such resources is through High-Performance Computing (HPC) centers. Many academic research institutions offer their own HPC Centers but struggle to make the computing resources easily accessible and user-friendly. Here we present SHABU, a RESTful Web API framework that enables S & E communities to access resources from Boston University’s Shared Computing Center (SCC). The SHABU requirements are derived from the use cases described in this work.
基金This work was supported by the National Natural Sciences Foundation.
文摘An inspection of the φ-ψ angle distribution strongly suggests that protein folding is highly constrained. A number of researchers have even suggested that a relatively small set of discrete φ-ψ regions might be sufficient to describe most protein conformation. The total of 541 tight turns from 101 non-identical proteins were extracted form Brookhaven DataBank. The dihedral values of tight turns were scattered into the seven regions on the Ramachandran plot. These seven regions were called A1, A2, B1, B2, B22, T1 and T2. A1 and A2 are the traditional a-helix regions, B1, B2 and B22 the β-strand regions, Tl and T2 the β-turn regions. The A2 and T2 regions were not defined as 'discrete' or single points but rather as one dimensional extended states. Based on the geometry of the two central residues of the tight turns, the new classification of β-turn was defined. This classification of the majority of β-turns fell into only six of the possible forty nine region combinations and were identifiable with the traditional nomenclature of Venkat-achalam(1), but much simpler.The function of β-turn in the conformation of proteins was studied. The hydrophobicity for different type turns was discussed. It shows that β-turns have very strong hydrophilic property, so they are usually situated at the folding protein surface. The features of β-turn and its amino acid distribution in this 541 β-turn group and different type β-turn were given.
