PROTEIN MODELING & STRUCTURAL GENOMICS

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 MMTSB资源的蛋白质建模项目的目标是开发一种多尺度建模方法，用于蛋白质结构预测，片段和环建模，以及通过其他方法获得的近似结构的结构细化。对于基于网格的低分辨率建模，使用Kolinski和Skolnick的MONSTER程序，并作为MMTSB工具集的一部分分发。在这个模型中，蛋白质被表示为一个单一的粒子为每个残基位于侧链中心，并模拟与蒙特卡罗计划上的立方晶格。最近，该项目已扩展到包括Skolnick实验室的最新一代结构预测工具PROSPECTOR 3/TASSER/SPICKER。使用CHARMM与基于广义玻恩近似的隐式溶剂模型进行全原子建模。这允许快速的能量评估的所有原子结构，并提供了快速的所有原子模拟的可能性，进一步的结构细化。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal of the protein modeling project of the MMTSB resource aims at developing a multi-scale modeling approach to protein structure prediction, fragment and loop modeling, as well as structure refinement of approximate structures derived by other methods. For lattice-based low-resolution modeling the MONSSTER program by Kolinski and Skolnick is used and distributed as part of the MMTSB Tool Set. In this model proteins are represented with a single particle for each residue located at the side chain center and are simulated with a Monte Carlo scheme on a cubic lattice. More recently, the project has been extended to include the newest generation structure prediction tools PROSPECTOR3/TASSER/SPICKER from the Skolnick lab. All-atom modeling is performed using CHARMM with an implicit solvent model based on a Generalized Born approximation. This allows rapid energy evaluations for all-atom structures and offers the possibility of fast all-atom simulations for further structure refinement.