134
123. Iriye R, Furukawa K, Nishida R, Kim C, Fukami H (1992) Isolation and synthesis of a new
bio-antimutagen, petasiphenol, from scapes of Petasites japonicum. Biosci Biotechnol Biochem. 56(11):1773–1775
124. Zhang X, Moréra S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg
MJ, Lindahl T, Freemont PS (1998) Structure of an XRCC1 BRCT domain: a new protein–
protein interaction module. EMBO J 17(21):6404–6411
125. Ketkar A, Zafar MK, Maddukuri L, Yamanaka K, Banerjee S, Egli M, Choi JY, Lloyd RS,
Eoff RL (2013) Leukotriene biosynthesis inhibitor MK886 impedes DNA polymerase activity. Chem Res Toxicol 26(2):221–232
126. Berman HM (2000) The protein data bank. Nucleic Acids Res 28:235–242
127. Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA,
James TL, Kuntz ID (2009) DOCK 6: combining techniques to model RNA-small molecule
complexes. RNA 15(6):1219–1230
128. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera—a visualization system for exploratory research and analysis. J
Comput Chem 25(13):1605–1612
129. Grosdidier A, Zoete V, Michielin O (2011) Fast docking using the CHARMM force field
with EADock DSS. J Comput Chem 32(10): 2149–2159
130. Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK
(2011) Human DNA polymerase eta is pre-aligned for dNTP binding and catalysis. J Mol
Biol 415: 627–634
131. Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) Watching DNA polymerase η
make a phosphodiester bond. Nature 487(7406):196–201
132. Beckman JW, Wang Q, Guengerich FP (2008) Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence. J Biol Chem
283(52):36711–36723
133. Eoff RL, Sanchez-Ponce R, Guengerich FP (2009) Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem 284(31):
21090–21099
134. Martin OA, Garro HA, Kurina Sanz MB, Pungitore CR, Tonn CE (2011) In silico study
of the inhibition of DNA polymerase by a novel catalpol derivative. J Mol Model 17(10):
2717–2723
135. Allouche AR (2011) Gabedit—a graphical user interface for computational chemistry softwares. J Comput Chem 32(1):174–182
136. Stewart JJ (2007) Optimization of parameters for semiempirical methods V: modification of
NDDO approximations and application to 70 elements. J Mol Model 13:1173–1213
137. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718
138. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4:
435–447
139. Schüttelkopf AW, van Aalten DM (2004) PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr D 60:1355–1363
140. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593
141. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (2004) Making optimal use
of empirical energy functions: force-field parameterization in crystal space. Proteins 57:
678–683
142. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W (2003) A point-charge force
field for molecular mechanics simulations of proteins based on condensed-phase quantum
mechanical calculations. J Comput Chem 24:1999–2012
143. Li Y, Korolev S, Waksman G (1998) Crystal structures of open and closed forms of binary
and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17:7514–7525
A. Yu. Nyporko
123. Iriye R, Furukawa K, Nishida R, Kim C, Fukami H (1992) Isolation and synthesis of a new
bio-antimutagen, petasiphenol, from scapes of Petasites japonicum. Biosci Biotechnol Biochem. 56(11):1773–1775
124. Zhang X, Moréra S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg
MJ, Lindahl T, Freemont PS (1998) Structure of an XRCC1 BRCT domain: a new protein–
protein interaction module. EMBO J 17(21):6404–6411
125. Ketkar A, Zafar MK, Maddukuri L, Yamanaka K, Banerjee S, Egli M, Choi JY, Lloyd RS,
Eoff RL (2013) Leukotriene biosynthesis inhibitor MK886 impedes DNA polymerase activity. Chem Res Toxicol 26(2):221–232
126. Berman HM (2000) The protein data bank. Nucleic Acids Res 28:235–242
127. Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA,
James TL, Kuntz ID (2009) DOCK 6: combining techniques to model RNA-small molecule
complexes. RNA 15(6):1219–1230
128. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera—a visualization system for exploratory research and analysis. J
Comput Chem 25(13):1605–1612
129. Grosdidier A, Zoete V, Michielin O (2011) Fast docking using the CHARMM force field
with EADock DSS. J Comput Chem 32(10): 2149–2159
130. Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK
(2011) Human DNA polymerase eta is pre-aligned for dNTP binding and catalysis. J Mol
Biol 415: 627–634
131. Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) Watching DNA polymerase η
make a phosphodiester bond. Nature 487(7406):196–201
132. Beckman JW, Wang Q, Guengerich FP (2008) Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence. J Biol Chem
283(52):36711–36723
133. Eoff RL, Sanchez-Ponce R, Guengerich FP (2009) Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem 284(31):
21090–21099
134. Martin OA, Garro HA, Kurina Sanz MB, Pungitore CR, Tonn CE (2011) In silico study
of the inhibition of DNA polymerase by a novel catalpol derivative. J Mol Model 17(10):
2717–2723
135. Allouche AR (2011) Gabedit—a graphical user interface for computational chemistry softwares. J Comput Chem 32(1):174–182
136. Stewart JJ (2007) Optimization of parameters for semiempirical methods V: modification of
NDDO approximations and application to 70 elements. J Mol Model 13:1173–1213
137. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718
138. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4:
435–447
139. Schüttelkopf AW, van Aalten DM (2004) PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr D 60:1355–1363
140. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593
141. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (2004) Making optimal use
of empirical energy functions: force-field parameterization in crystal space. Proteins 57:
678–683
142. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W (2003) A point-charge force
field for molecular mechanics simulations of proteins based on condensed-phase quantum
mechanical calculations. J Comput Chem 24:1999–2012
143. Li Y, Korolev S, Waksman G (1998) Crystal structures of open and closed forms of binary
and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17:7514–7525
A. Yu. Nyporko