Interaction of antibodies with aromatic ligands: the role of pi-stacking [0.03%]
抗体与芳香配体的相互作用：π-堆叠的作用
Vladimir Arzhanik,Darja Svistunova,Oleg Koliasnikov et al.
Vladimir Arzhanik et al.
Antibodies are responsible for antigen recognition in vertebrate organisms. Practically any molecule can be bound by antibodies. In this work structures of 73 complexes of antibodies with small antigens were taken from PDB database and comp...
Identification of conserved features of LAGLIDADG homing endonucleases [0.03%]
鉴定LAGLIDADG同源内切酶的保守特征
Alexander Grishin,Ines Fonfara,Andrei Alexeevski et al.
Alexander Grishin et al.
LAGLIDADG family of homing endonucleases are rare-cutting enzymes which recognize long target sequences and are of great interest in genome engineering. Despite advances in homing endonuclease engineering, effective methods of broadening th...
GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families [0.03%]
糖苷水解酶家族GH101：亚家族结构与其他家族的进化关系
Daniil G Naumoff
Daniil G Naumoff
The GH101 family is composed of endo-alpha-N-acetylgalactosaminidases and their homologues. Pairwise sequence comparison and phylogenetic analysis allowed us to distinguish five to six subfamilies in this family. Diverse domain structures w...
Sergei Rahmanov,Ivan Kulakovskiy,Leonid Uroshlev et al.
Sergei Rahmanov et al.
Empirical potentials for interaction of proteins with intracellular ions are presented. We derive the potentials using a training dataset of the protein 3D structure bank, PDB, based on the statistical analysis of contacts between ions and ...
Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA [0.03%]
Deppdb—DNA静电势性质数据库：基因组DNA的静电性质
Alexander A Osypov,Gleb G Krutinin,Svetlana G Kamzolova
Alexander A Osypov
The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB--DNA Electrostatic Potential Properties Database--was developed to hold...
A comparative analysis of folding pathways of thermophilic and mesophilic proteins by Monte Carlo simulations [0.03%]
利用蒙特卡罗模拟对嗜热蛋白和中温蛋白质折叠途径进行比较分析
Anna V Glyakina,Oxana V Galzitskaya
Anna V Glyakina
In this work we have studied the folding pathways for four pairs of homologous proteins from thermophilic and mesophilic organisms from two different structural classes (class a, all-alpha proteins and class d, alpha + beta proteins) using ...
Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method [0.03%]
基于Molecular Dynamics和FoldUnfold方法的中温蛋白及嗜热同源蛋白的柔性与可移动性研究
Tatyana B Mamonova,Anna V Glyakina,Maria G Kurnikova et al.
Tatyana B Mamonova et al.
To function properly protein molecules require both flexibility and rigidity, therefore fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. In this work we used two theoretical a...
Hierarchical classification of gene ontology terms using the GOstruct method [0.03%]
利用GOstruct方法对基因本体论术语进行分层分类
Artem Sokolov,Asa Ben-Hur
Artem Sokolov
Protein function prediction is an active area of research in bioinformatics. Yet, the transfer of annotation on the basis of sequence or structural similarity remains widely used as an annotation method. Most of today's machine learning app...
Combinatorial reconstruction of half-sibling groups from microsatellite data [0.03%]
基于微卫星数据的半同胞组系的组合重构方法
Saad I Sheikh,Tanya Y Berger-Wolf,Ashfaq A Khokhar et al.
Saad I Sheikh et al.
While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a fo...
Characterizing the space of interatomic distance distribution functions consistent with solution scattering data [0.03%]
与溶液散射数据一致的原子间距离分布函数的空间特征
Paritosh A Kavathekar,Bruce A Craig,Alan M Friedman et al.
Paritosh A Kavathekar et al.
Scattering of neutrons and X-rays from molecules in solution offers alternative approaches to the study of a wide range of macromolecular structures in their solution state without crystallization. We study one part of the problem of elucid...