naccess 2.1.1 Atomic Solvent Accessible Area Calculation Software: Developed at UCL by Simon Hubbard and Janet Thornton, this program calculates absolute and relative surface accessibilities of protein and nucleic acid structures. The program can also be used in conjunction with the Ligplot program to provide information on buried and accessible residues. naccess is a program that automatically performs accessible area calculation of a molecule from a standard Protein Data Bank (PDB) file input. The output includes a file of atomic accessible areas, a file of summed absolute and relative residue accesible areas, and a calculation log file.The algorithm is based on work described in the paper of Lee and Richards as referenced below. Program author Simon Hubbard curently holds the position of Professor in the Faculty of Life Sciences at Manchester University.
Keywords for this software
References in zbMATH (referenced in 8 articles )
Showing results 1 to 8 of 8.
- Simon Mitternacht: FreeSASA: An open source C library for solvent accessible surface area calculations (2016) arXiv
- Gameiro, Marcio; Hiraoka, Yasuaki; Izumi, Shunsuke; Kramar, Miroslav; Mischaikow, Konstantin; Nanda, Vidit: A topological measurement of protein compressibility (2015)
- Chen, Ruoying; Zhang, Zhiwang; Wu, Di; Zhang, Peng; Zhang, Xinyang; Wang, Yong; Shi, Yong: Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming (2011)
- Guharoy, Mainak; Chakrabarti, Pinak: Conserved residue clusters at protein-protein interfaces and their use in binding site identification (2010) ioport
- Liu, Qian; Li, Jinyan: Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective (2010) ioport
- Montuori, Alfonso; Raimondo, Giovanni; Pasero, Eros: An information theoretic approach for improving data driven prediction of protein model quality (2008)
- Tobi, Dror; Bahar, Ivet: Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? (2007) ioport
- Saraboji, K.; Gromiha, M. Michael; Ponnuswamy, M. N.: Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes (2005)