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1.
Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease.  相似文献   
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We present analytical formulae for the first and second derivatives of the Helmholtz free energy of non-relativistic ideal Fermi gas. Important thermodynamic quantities such as heat capacity, sound velocity, heat capacity ratio, and others are explicitly expressed through the derivatives. We demonstrate correct ideal Boltzmann gas and low-temperature Fermi gas asymptotes and derive corrections to thermodynamic functions for these limiting cases. Numerical computations of thermodynamic properties of ideal Fermi gas can be accurately performed using the developed freely available Python module ifg .  相似文献   
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A tool for the automated assembly, molecular optimization and property calculation of supramolecular materials is presented. stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes. stk currently supports the construction of linear polymers, small linear oligomers, organic cages in multiple topologies and covalent organic frameworks (COFs) in multiple framework topologies, but is designed to be easy to extend to new, unrelated, supramolecules or new topologies. Extension to metal–organic frameworks (MOFs), metallocycles or supramolecules, such as catenanes, would be straightforward. Through integration with third party codes, stk offers the user the opportunity to explore the potential energy landscape of the assembled supramolecule and then calculate the supramolecule's structural features and properties. stk provides support for high‐throughput screening of large batches of supramolecules at a time. The source code of the program can be found at https://github.com/supramolecular-toolkit/stk . © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.  相似文献   
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摘 要:针对我国目前土沉降监测的自动化程度及仪器可靠性低、监测数据不及时、测量精度不高等问题,提出了一种新型基于霍尔效应的科学监测方法。这种方法采用多个霍尔器件组成阵列,将沉降磁环分布在土中,土的沉降会带动沉降磁环的跟随沉降,于是便会引起霍尔器件周围磁场强度发生相应的变化。利用霍尔效应监测霍尔器件周围磁场强弱并转化为相应的电信号,采用RS485总线通讯方式将采集到的数据实时上传至实验主机,主机对实验数据进行科学建模处理找到沉降磁环沉降位移与电信号的关系,并设计监测管理平台以实现对土沉降实时在线监测。通过实验验证这种监测方法监测精度高最大误差在0.4mm、稳定性好,可以对多点实时在线监测,从而实现对土沉降的智能化高精度监测。在设计中可结合当前远程传输控制技术实现数据远程共享,具有更加广泛的应用前景。  相似文献   
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We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.  相似文献   
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缅甸蟒蛇腹鳞表面的摩擦机理及摩擦各向异性研究   总被引:1,自引:0,他引:1  
采用原子力显微镜观察缅甸蟒蛇腹鳞表面的微观结构,采用UMT-2型摩擦磨损试验机研究不同载荷及运动方向的腹鳞表面的宏观摩擦各向异性,建立了摩擦运动的接触模型,分析了腹鳞表面的磨损机理.结果表明:腹鳞表面的微观结构由指状微突体和板结构部分周期排列而成,其结构可用9个特征参数定量描述;腹鳞表面摩擦力由分子作用力、表面微突体的犁沟力、楔形作用力以及材料弹性滞后共同引起;腹鳞表面的摩擦系数在0.07左右并与运动方向有关,摩擦系数随载荷增加而减小;后向运动及左、右侧向运动时摩擦系数基本相等,比前向运动时高33%左右;腹鳞表面微突体不同方向上倾斜角度的差异是引起摩擦各向异性的主要原因.研究结果对仿生制造摩擦各向异性表面提供实验依据.  相似文献   
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Herein, we investigated the viability of two group additivity methods for predicting Gibbs energies of a set of uranyl complexes. In first place, we proved that both density functional theory (DFT)-based methods and Serezhkin's stereoatomic model provide equivalent answers in terms of stability. Moreover, we proposed a novel methodology based on Mayer's population analysis for estimating Serezhkin's empirical parameters theoretically. On the other hand, we showed that Cheong and Persson linear algebra methodology can be successfully applied to uranyl complexes, and analyzed its performance in connection with the chemical nature of the compounds employed in the model.  相似文献   
10.
In this paper we continue our study of the dual SL(2,C)SL(2,C) symmetry of the BFKL equation, analogous to the dual conformal symmetry of N=4N=4 super-Yang–Mills. We find that the ordinary and dual SL(2,C)SL(2,C) symmetries do not generate a Yangian, in contrast to the ordinary and dual conformal symmetries in the four-dimensional gauge theory. The algebraic structure is still reminiscent of that of N=4N=4 SYM, however, and one can extract a generator from the dual SL(2,C)SL(2,C) close to the bi-local form associated with Yangian algebras. We also discuss the issue of whether the dual SL(2,C)SL(2,C) symmetry, which in its original form is broken by IR effects, is broken in a controlled way, similar to the way the dual conformal symmetry of N=4N=4 satisfies an anomalous Ward identity. At least for the lowest orders it seems possible to recover the dual SL(2,C)SL(2,C) by deforming its representation, keeping open the possibility that it is an exact symmetry of BFKL. Independently of a possible relation to N=4N=4 scattering amplitudes, this opens an avenue for explaining the integrability of BFKL in terms of two finite-dimensional subalgebras.  相似文献   
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