Analytical and Biological Chemistry Research Facility, University College Cork, Western Road, Cork, Co, Cork, Ireland.
J Cheminform. 2011 Mar 16;3:8. doi: 10.1186/1758-2946-3-8.
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion.
Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol.
Confab is available from http://confab.googlecode.com.
许多计算化学分析需要生成构象，要么是即时生成，要么是预先生成。我们提出了 Confab，这是一个开源的命令行应用程序，用于根据多样性标准系统地生成低能量构象。
Confab 使用“扭转驱动方法”生成构象，该方法涉及对每个可旋转键的一组允许扭转角度进行系统迭代。能量使用 MMFF94 力场进行评估。多样性使用相对于已经存储的构象的重原子均方根偏差 (RMSD) 进行测量。我们研究了从蛋白质数据库中包含 1000 个配体的数据集恢复晶体结构的情况，该数据集的构象数少于 100 万个。在多样性水平为 1.5Å 且能量截止值为 50kcal/mol 的情况下，Confab 可以将 97%的分子恢复到 1.5Å 以内。
Confab 可从 http://confab.googlecode.com 获取。
Zotero 插件
