Exact enumeration of conformations for two and three dimensional lattice proteins

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• 作者：K. Silpaja Chandrasekar ; M.V. Sangaranarayanan ; ^{sangara@iitm.ac.in" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Lattice proteins ; Hydrophobic-Polar model ; Self-avoiding walks ; Conformations ; Polymers
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：199
• 期：Complete
• 页码：8-11
• 全文大小：1372 K

文摘

We report an efficient methodology for exactly enumerating conformations of lattice proteins, taking into account the self-avoiding nature. These self-avoiding walks in square and simple cubic lattices take into account, the detailed paths by which a destination site can be reached from a starting site. The strategy employing JAVA programming enables the exact enumeration for very large lattice sizes. The estimation of these conformations is helpful in designing the protein sequences pertaining to Hydrophobic-Polar models.

Program summary

Program title: Exact enumeration of conformations in lattice proteins

No of lines in distributed program: 1027

No of bytes in distributed program: 51698

Programming language: JAVA

Computer: Tested on Intel^®Core(TM) i5-4570. Will function on any computer with JAVA compilers.

Operating system: Tested on Microsoft Windows 7 Professional. Should run on any platform with JAVA

Has the code been vectorized or parallelized? : No

RAM: Depends on the system size.

Nature of the problem: The problem involves the enumeration of the conformation of lattice proteins for various amino acid chain lengths by considering them as self-avoiding walks. The methodology is illustrated for square and simple cubic lattices.

Solution method: The code was implemented using the nodes as in a tree which was arranged in the stack. Each element is visited once and is moved to the next node. The process is repeated till all nodes are visited and the process terminates when a site is revisited.

Restrictions: Runs only in JAVA compilers

Running time: Depends on the system size. Using 4 processors, the output leading to entries in Tables 1 and 2 was generated within one minute.

The listing of the codes and the output of the program are provided in the Supporting Information.