Spatial Decomposition of Translational Water–Water Correlation Entropy in Binding Pockets
نویسندگان
چکیده
منابع مشابه
Spatial Decomposition of Translational Water–Water Correlation Entropy in Binding Pockets
A number of computational tools available today compute the thermodynamic properties of water at surfaces and in binding pockets by using inhomogeneous solvation theory (IST) to analyze explicit-solvent simulations. Such methods enable qualitative spatial mappings of both energy and entropy around a solute of interest and can also be applied quantitatively. However, the entropy estimates of exi...
متن کاملPair-correlation entropy of hydrophobic hydration: decomposition into translational and orientational contributions and analysis of solute-size effects.
We develop an efficient method to evaluate the translational and orientational contributions to the solute-water pair-correlation entropy that is a major component of the hydration entropy. A water molecule is modeled as a hard sphere of diameter dS=0.28 nm in which a point dipole and a point quadrupole of tetrahedral symmetry are embedded. A hard sphere of diameter dM, a hydrophobic solute, is...
متن کاملModular architecture of nucleotide-binding pockets
Recently, modularity has emerged as a general attribute of complex biological systems. This is probably because modular systems lend themselves readily to optimization via random mutation followed by natural selection. Although they are not traditionally considered to evolve by this process, biological ligands are also modular, being composed of recurring chemical fragments, and moreover they e...
متن کاملA new method for rapid comparison of protein binding pockets by capturing spatial distributions
Efficient determination of structural similarities between protein binding pockets is an important challenge in computational chemistry. A degree of similarity in the mutual comparison is often estimated in terms of graphs and by calculating a metric such as the maximum shared common subgraph. Cavbase [1] was developed as a tool for the automatic detection, storage and classification of putativ...
متن کاملsurvey microbial decomposition leaf litter of salix sp. populus sp. robinia sp. in artificial stream
مطالعه اکولوژیک از سرچشمه رودخانه قره سو(سراب روانسر) در استان کرمانشاه واقع در غرب ایران در پائیز 1378 انجام شد، حداکثر دمای آب 20 درجه سانتی گراد بود، هنگام مطالعه دما در سرچشمه 18 سانتی گراد بود، مقدار عناصر شیمیایی آب اندازه گیری نشد. در این پژوهش لاشبرگ های درختی از بید، چنار، اقاقیا جمع آوری سپس توسط بخش هرباریوم دانشکده کشاورزی دانشگاه شناسایی شدند. وزن خاکستر خشک afdm در(نمونه برداری ...
15 صفحه اولذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2015
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.5b00939