MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks

被引：21

作者：

Bystroff, C ^{[1
]}

机构：

[1] Rensselaer Polytech Inst, Dept Biol, Troy, NY 12180 USA

来源：

PROTEIN ENGINEERING | 2002年 / 15卷 / 12期

关键词：

binary operations; hydrophobic effect; implicit solvent; molecular graphics; molecular simulations; molecular surface; water;

D O I：

10.1093/protein/15.12.959

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A fast algorithm for computing the solvent-accessible molecular surface area (SAS) using Boolean masks [Le Grand,S.M. and Merz,K.M.J. (1993). J. Comput. Chem., 14, 349-352) has been modified to estimate the solvent-excluded molecular surface area (SES), including contact, toroidal and re-entrant surface components. Numerical estimates of arc lengths of intersecting atomic SAS are used to estimate the toroidal surface and intersections between those arcs are used to estimate the re-entrant surface area. The new method is compared with an exact analytical method. Boolean molecular surface areas are continuous and pairwise differentiable and should be useful for molecular dynamics simulations, especially as the basis for an implicit solvent model.

引用

页码：959 / 965

页数：7

共 24 条

[1] AN EVALUATION OF IMPLICIT AND EXPLICIT SOLVENT MODEL SYSTEMS FOR THE MOLECULAR-DYNAMICS SIMULATION OF BACTERIOPHAGE-T4 LYSOZYME [J].

ARNOLD, GE ;

ORNSTEIN, RL .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1994, 18 (01) :19-33

[2] Recent changes to RasMol, recombining the variants [J].

Bernstein, HJ .

TRENDS IN BIOCHEMICAL SCIENCES, 2000, 25 (09) :453-455

[3] THE MOLECULAR-SURFACE PACKAGE [J].

CONNOLLY, ML .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1993, 11 (02) :139-143

[4] SOLVENT-ACCESSIBLE SURFACES OF PROTEINS AND NUCLEIC-ACIDS [J].

CONNOLLY, ML .

SCIENCE, 1983, 221 (4612) :709-713

[5]

Coxeter H. S. M., 1961, INTRO GEOMETRY

[6] Molecular simulation study of cooperativity in hydrophobic association [J].

Czaplewski, C ;

Rodziewicz-Motowidlo, S ;

Liwo, A ;

Ripoll, DR ;

Wawak, RJ ;

Scheraga, HA .

PROTEIN SCIENCE, 2000, 9 (06) :1235-1245

[7] Evaluation of a fast implicit solvent model for molecular dynamics simulations [J].

Ferrara, P ;

Apostolakis, J ;

Caflisch, A .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 46 (01) :24-33

[8] An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution [J].

Fraternali, F ;

vanGunsteren, WF .

JOURNAL OF MOLECULAR BIOLOGY, 1996, 256 (05) :939-948

[9]

GOGONEA V, 1994, J MOL STRUC-THEOCHEM, V311, P305

[10] Discrimination of the native from misfolded protein models with an energy function including implicit solvation [J].

Lazaridis, T ;

Karplus, M .

JOURNAL OF MOLECULAR BIOLOGY, 1999, 288 (03) :477-487

← 1 2 3 →