Sobolev V, Sorokine A, Prilusky J, Abola E E, Edelman M
Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel.
Bioinformatics. 1999 Apr;15(4):327-32. doi: 10.1093/bioinformatics/15.4.327.
New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein.
Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues. Our approach is based on a detailed analysis of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-accessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of the ligand.
Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.
已设计出新型软件，以协助分子生物学家理解修饰配体和/或蛋白质的结构后果。
描述了用于分析配体 - 蛋白质接触（LPC软件）和结构单元接触（CSU软件）的工具，这些结构单元如螺旋、片层、链和残基。我们的方法基于对原子间接触和界面互补性的详细分析。对于任何配体或结构单元，这些软件会自动：（i）计算每个原子的溶剂可及表面；（ii）确定接触的残基及其所经历的相互作用类型（疏水 - 疏水、芳香 - 芳香等）；（iii）指出所有可能的氢键。LPC软件还可预测配体化学修饰后结合强度的变化。
LPC和CSU均可通过蛋白质数据银行（PDB）访问，并集成在所有PDB文件的3DB图谱页面中。对于任何给定文件，也可分别通过在网址http://www.pdb.bnl.gov/pdb-bin/lpc?PDB_ID= 和http://www.pdb.bnl.gov/pdb-bin/csu?PDB_ID= 的末尾添加四字母PDB代码来访问这些工具。最后，可通过http://sgedg.weizmann.ac.il/lpc 和http://sgedg.weizmann.ac.il/csu访问LPC和CSU。
