[Post] Drug Design Software [schroinger] All manual

Drug Design Software [Schrodinger] All manual

Schr & ouml; Inger (SCHR) is a complete software package for drug discovery, including: Receptor-based and compound-based induction matching and flexible docking modes; binding modes based on the receptor structure and the polarity of the complexes; docking mode based on Receptor structure and solution environmental properties; combination chemical database design and combination database-based docking mode; Drug Design Based on the Combination Structure, efficacy group and 3d-qsar; biological molecular structure simulation, protein, sugar, nucleic acid, small peptide, etc.; target-based drug design; adme properties prediction.

Schrodinger is a complete solution for drug discovery:

(1) high-throughput Virtual Screening: the virtual screening function of schödnex software can screen 1.5 million compounds on 35 CPU clusters every day. Provides an all-in-one setting interface that allows you to define specific properties to filter out compounds that do not meet the needs. required modules: glide, ligprep, qikprop, epik, sitemap, and liaision;

(2) Precise Interconnection: For the enriched compound library after virtual screening or the user's own specific compound library, the following two real environments can be considered by using the precise interconnection mode provided by schödnex software, the obtained accuracy results can match the experiment results:

(1) Induction of binding molecules on protein activity site structure (induced fit); required modules: glide, Prime, liaison, sitemap, epik, macromodel, ligprep, qikprop;

(2) protein molecules induce the polarization of binding molecules (qpld). required modules: glide, liaison, sitemap, epik, macromodel, qsite, ligprep, jaruar, qikprop;

(3) efficacy group and 3d-qsar: the solution of the efficacy group and 3d-qsar provided by schödör, without receptor information

In the case of information, researchers can use the information of active complexes to design new drugs. required modules: phase, confgen, ligprep, macromodel, strike;

(4) All-New Drug Design (de novo design): the me-too and me-better drug design solutions provided by the schörödnex software allow users to replace the side chains or mother cores of known compounds; required modules: combiglide, glide, ligprep, qikprop;

(5) enzyme catalysis and metal enzyme Research (QM/mm method): The QM/mm method provided by schörödnex software can take into account the chemical reaction of Protein Active Sites. Required modules: qsite and jaruar;

(6) biological molecular structure simulation: precise protein, nucleic acid, and polysaccharide structures can be created. Prime and macromodel modules are required;

(7) adme properties prediction: Used in pharmacological research; required module: qikprop;

(8) Chemical Informatics: the solution of chemical informatics provided by schörödnex software provides the following professional algorithms: Binary fingerprint vector clustering analysis; similarity analysis; hierarchical clustering method; Chemical filtering method; Diversity Analysis; sphere exclusion diversity; Word Structure search; unique smiles generation method; multivariate linear regression; partial least squares regression; principal component analysis; Principal Component Regression Analysis; neural network algorithm; naive Bayes analysis algorithm; self-organizing Feature ing; required module: canvas;

Introduction to the modules contained in schroinger:

Glide: a precise docking tool for the binding of the compound and receptor. Glide provides Sp (Standard precision) and XP (extra precision) methods to provide speed and accuracy for drug discovery. Based on the SP (Standard precision) high-precision docking with hundreds of thousands of complexes, XP (extra precision) mode can further test the SP docking result to reduce false positive. Glidescore can effectively reduce false positives and increase the enrichment rate by taking into account the contribution of lipid, hydrogen bond, and metal complexes, as well as the rotation of unsuitable keys and the space exclusion of atoms. In addition, the SP-QPLD and XP-QPLD scores can consider the extremely sexual orientation of the donor in the body. Glide and prime modules can be used together to implement the induced fit function.

Maestro: it is the unified interface of Schr & ouml; dinger software. The powerful image display function enables researchers to clearly observe the most complex research system.

Prime: a precise protein structure prediction package. Prime can create a high-precision receptor model to ensure the success of drug development in the future. Prime can accurately create the loop area. It contains two methods: Same-source mode and threading.

Liaison: A Precise Computation Program for the binding energy of the receptor, liaison predicts the binding energy in ~ The experimental value of 1 kcal/mol can be applied to situations where the degree of freedom of the complexes is relatively large.

Sitemap: a precise protein activity site authentication tool. There are two functions: active site location and chemical characteristics analysis of active sites.

Combiglide: design an enriched combination library for a target or a type of target, and use the target structure to implement a virtual screening program based on the combination library. Filter compounds by specific settings, such as adme prediction. And implement de novo design.

Epik: quick and accurate prediction of Ka. Epik is able to obtain the Ka value and a 3D structure file, including multiple variants and possible ionic states under special conditions, in the solution of water and dsmo, it can also accurately calculate the Ka value. It can effectively improve the screening accuracy.

Macromodel: a gold standard based on the force field model. The processing systems include organic compounds, sugar, nucleic acid, small peptide, and protein. In the study of protein-binding complexes, the active site is allowed to be sufficiently flexible while other locations are rigid.

Qsite: High-Performance QM/mm computing program. Qsite applies quantum mechanics computing to the active center of the active site of the protein, and applies molecular dynamics to the residual protein system, which is a powerful tool for pilot optimization. It can be applied to the catalytic reaction of enzymes involved in Electron Transfer and the metal-containing System of protein activity centers.

Phase: the complete toolkit for the most accurate drug group creation. Phase can be used to set the rejection balls Based on the complexes. Assume that some regions are occupied by proteins, so that the space shapes are not matched. The efficacy group search database can be generated based on the crystal structure of the body in the compound structure of the receptor. With powerful data management capabilities, phase allows users to generate and store databases with multiple concurrencies for filtering at any time during work. The confgen technique was used to investigate the molecules involved in the complexes, including key rotation, and calculation of the energy of each constructor to preserve a reasonable constructor.

Strike: A Tool for statistical models and QSAR. Strike is a tool for building a structure-activity relationship model. Strike can use this model to quickly predict the activity of compounds or predict the image properties of large virtual libraries.

Qikprop: a fast and accurate adme prediction tool. Designed by Professor Bill Jorgensen from Yale University. It can predict the 3D structure of the entire molecule. The predicted properties include: log ps, log s, log BB of octyl alcohol/water and water/gas; the activity of the whole central system; Permeability of Caco-2 and MDCK cells; serum albumin binds to active log khsa, and K-ion channel of HERG for latent log ic50.

Ligprep: a precise tool for converting 2D to 3D structures. Effective and accurate 2D to 3D conversion is the first step in successful drug design. ligprep can produce a variety of concurrencies from a single structure in chemistry and structure. Ligprep can be glide, qikprop, and phase to generate input files. To meet the needs of the simulation program, the special settings provided by ligprep can optimize the output structure.

Primex: Refined crystal structure of protein x-ray. Including correct placement of the compound, construction of the loop area, and simulated annealing.

Jaguar: A Fast first-principle Electronic Structure computing package that can introduce the accuracy of quantum chemistry into life science research.
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