ADSBET2：盐桥能量项自动测定版本2
ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2.
作者信息
Nayek Arnab, Gupta Parth Sarthi Sen, Banerjee Shyamashree, Sur Vishma Pratap, Seth Pratyay, Das Sunit, Islam Rifat Nawaz Ul, Bandyopadhyay Amal Kumar
机构信息
Authors equally contributed.
Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India.
出版信息
Bioinformation. 2015 Aug 31;11(8):413-5. doi: 10.6026/97320630011413. eCollection 2015.
UNLABELLED
Component (bridge: ΔΔGbrd , background: ΔΔGprot , desolvation: ΔΔGdsolv ) and net (ΔΔGnet ) energy-terms of salt-bridge-structure (SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS) method. While the procedure reports gross energy terms (Kcal Mol(-1) ), report on bond-multiplicity corrected normalized energyterms (Kcal Mol(-1) Bond(-1) ) along with their accessibility (ASA) in monomer, isolated-SBS (ISBS) and networked-SBS (NSBS) format would be very useful for statistical comparison among SBSs and understanding their location in protein structure. In this end, ADSBET2 potentially incorporates these features along with additional model for side-chain. Gross and normalized energy-terms are redirected in monomer, ISBS and NSBS format along with their ASA informations. It works on any number of SBSs for any number of structure files present in a database. Taken together, ADSBET2 has been suitable for statistical analyses of SBSs energetics and finds applications in protein engineering and structural bioinformatics.
AVAILABILITY
ADSBET2 is freely available at http://sourceforge.net/projects/ADSBET2/ for all users.
未标注
盐桥结构（SBS）的组成部分（桥：ΔΔGbrd，背景：ΔΔGprot，去溶剂化：ΔΔGdsolv）和净能量项（ΔΔGnet）由程序ADSBET自动生成，该程序利用通用的自适应泊松玻尔兹曼求解器（APBS）方法。虽然该程序报告总能量项（千卡摩尔⁻¹），但报告经键多重性校正的归一化能量项（千卡摩尔⁻¹键⁻¹）及其在单体、孤立盐桥结构（ISBS）和网络化盐桥结构（NSBS）形式中的可及性表面积（ASA），对于盐桥结构之间的统计比较以及理解它们在蛋白质结构中的位置将非常有用。为此，ADSBET2可能纳入了这些特征以及侧链的附加模型。总能量项和归一化能量项以单体、ISBS和NSBS形式重定向，并附带其ASA信息。它适用于数据库中存在的任何数量的结构文件中的任意数量的盐桥结构。综上所述，ADSBET2适用于盐桥结构能量学的统计分析，并在蛋白质工程和结构生物信息学中得到应用。
可用性
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