COSMOsim3D and COSMOsar3D 生命科學軟體-生化統計分析軟體/新永資訊有限公司

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COSMOsim3D and COSMOsar3D 生命科學軟體

COSMOsim3D and COSMOsar3D 生命科學軟體

  • COSMOsim3D and COSMOsar3D 生命科學軟體
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    生化統計分析軟體
  • 介紹
    The COSMO-RS method has proven the σ-profiles as the crucial information for most ADME properties as solubility, blood-brain-partition coefficients, and intestinal absorption, and even for many adsorption phenomena. Considering this fundamental importance of the σ-profiles for surface interactions of molecules in liquid states, they most likely also carry a large part of information required for the estimation of desolvation and binding processes, which are responsible for the inhibition of enzyme receptors by drug molecules. Thus a high similarity with respect to the σ-profiles appears to be
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COSMOsim3D

Based on the fact that ligands similar to an active ligand show an increased probability to be also active, ligand-based drug design does not require a target structure. The art of ligand-based drug design thus consists of finding adequate representations of the intermolecular interaction patterns of ligands defining a meaningful similarity measure. Typically, the similarity between ligand molecules is assessed in terms of two- or three-dimensional structure, shape, polar interactions, and pharmacophoric models.

COSMOsim3D is a unique and very robust method for automatic and unsupervised field-based ligand-ligand alignment and similarity searches. It utilizes local σ-profiles, which have been proved to contain the required information on the relevant molecular interactions.

The molecular surface charge approach of COSMOsim3D naturally enables scaffold hopping. Thus, the COSMOsim3D method is suited for datasets with different chemotypes, allowing users to find alternative chemical scaffolds with similar shape and polar features.

Key features:
  • • Pairwise alignment and similarity assessment: COSMOsim3D utilizes LSPs instead of chemical structure or pharmacophores to assess a molecule’s similarity to a template molecule. This enables scaffold hopping and allows users to deal with datasets of different chemotypes.
  • • Multi-template alignment: It is possible to align multiple template molecules and use their superposition as a virtual template molecule. The virtual template molecule can be used for alignment and similarity assessment of potential ligand molecules.
  • • Ligand-Based virtual screening: COSMOsim3D can be used to rank a set of potential ligand molecules according to their similarity to a single template or a virtual template stemming from the superposition of multiple ligands. Thus, it allows users to enrich ligand sets with potential cognate drugs, generating fewer false positives and more true hits.
 

COSMOsar3D

As an alternative approach to similarity-based ligand assessment, QSAR models are used to correlate computed properties of molecules and their biological activity. COSMOsar3D is an extension of COSMOsim3D which uses the LSPs of aligned ligands as a novel set of molecular interaction fields for 3D-QSAR.

In a recent study, LSP-based COSMOsar3D models instantly had a significantly higher predictivity than standard 3D QSAR models. Utilizing smooth spatial histograms introduces an increased robustness of the models against small geometrical shifts of the ligands relative to the grid even at larger grid spacing. In a histogram, a local property hotspot is smoothly partitioned over the neighboring grid points, resulting in a position-independent representation.

Key features:
  • • Robustness and Predictivity: Instead of using properties directly as input for MFA, COSMOsar3D uses a histogram of a property. This approach leads to very robust performance of the models with respect to grid size, grid position and small misalignments, while retaining increased predictive accuracy.
  • • Ionic and Neutral Molecules: The polarization charge densities of neutral and charged species are in the same range, which allows for the inclusion of compounds of varying charge states in the same model.
  • • Linear Relationship of logKi and LSPs: LSPs constitute an optimally suited set of descriptors for a linear regression analysis of pKi values, according to the 3D-QSAR paradigm. COSMOsar3D provides a rationale that logKi values should be linear functions of the LSP descriptors. To the best of our knowledge, no other set of molecular fields used so far in MFA can claim such a sound theoretical justification for the expectation of a linear pKi model.
  • • Description of Hydrogen Bonding: As shown in a recent paper, the polarization charge densities σ are better suited for the description of hydrogen bonding than the electrostatic potential, which is usually employed in MFA. See also “Polarization charge densities provide a predictive quantification of hydrogen bond energies.”
 

COSMOsim3D & COSMOsar3D

Local σ-profiles
Justified by the general COSMO-RS finding that intermolecular interactions can be excellently quantified based on the COSMO surface polarization densities σ, COSMOsim3D introduces local σ-profiles (LSPs) for the alignment and similarity measure of ligands. LSPs are σ-histograms, resulting from projecting the molecular σ-surface onto a 3D-grid, and they provide information about
  • • electrostatics
  • • hydrogen bonding
  • • hydrophobic interactions
  • • shape
Using LSPs, COSMOsim3D meanwhile has been proven to be a very accurate and extremely robust method for automatic and unsupervised field-based ligand-ligand alignment and similarity searching.
 
 

TURBOMOLE 7.5 化學計算軟體

Turbomole被認為是進行HF，DFT，MP2計算最快最穩定的代碼之一。它的特色不是在於新方法和新功能，而在於解決如何用盡量短的時間和 盡量少的內存需求，快速、穩定地處理工業應用型的分子。特別是它獨有的RI-DFT方法，據稱可以較其它大多數DFT程序節省10倍的CPU時間，因此非 常適合於大分子計算或中等分子的重複性計算（如幾何優化）

TURBOMOLE 7.5 化學計算軟體

FlexPDE 7 偏微分有限元素軟體

FlexPDE是一個有彈性的,易學,一般的目的用途的有限元素軟件,FlexPDE可獲得偏微分方程的數值解，偏微分方程在工程上常見於，物理、電機、電子、通訊、土木、機械、化工、化學、生物學、地質學、數學和其它科學領域FlexPDE使用這超強有限元素方法獲得數值解。然而，使用FlexPDE並不需要了解複雜的有限元素方法。

FlexPDE 7 偏微分有限元素軟體

COSMOtherm 量子化學軟體

COSMOtherm 是液體預測特性計算的通用工具，以獨特的方式結合了量子化學和熱力學。它計算幾乎任何純液體或混合液體中幾乎任何分子在可變溫度下的化學勢，即它預測分子在特定液體環境中的快樂程度。這是預測工業應用或學術研究所需的多種特性的關鍵，包括溶解度、分配、蒸氣壓和完整的相圖。與其他幾種可用方法相比，COSMOtherm 能夠通過應用熱力學一致方程來預測作為濃度和溫度函數的特性。

COSMOtherm 量子化學軟體