Schrödinger.v2015-2 Module

• Installation Guide

• Virtual Screening Workflow

• aacg - A Brief Guide to All-Atom/Coarse Grain Simulations

• BioLuminate - A comprehensive modeling package for biologics

  • Protein-protein docking

  • Antibody structure prediction, including both look-up and advanced loop modeling

  • Residue scanning for affinity, stability, and other properties (mutation analysis)

  • Cysteine scanning to add and remove disulfides

  • Fast homology modeling

  • Advanced homology modeling

  • Binding site detection and druggability assessment

  • Automated identification of reactive hot spots (oxidation, deamidation, etc.)

  • Advanced sequence viewer with full annotation and alignment facilities

  • Loop and residue mutation tools

  • Consensus viewer tool to rapidly identify common structural elements in related proteins

  • Low normal mode analysis

  • Advanced molecular mechanics conformational sampling

  • Alpha-helix stability assessment based on molecular dynamics

  • Full access to Schrödinger’s ligand-based tools and other Schrödinger program

• Canvas - A comprehensive cheminformatics computing environment

• CombiGlide – Interactive Enumeration and Docking Panel

• ConfGen - Accurate and efficient bioactive conformational searching

• Core Hopping - Comprehensive ligand- and receptor-based scaffold exploration for lead optimization

• Desmond - High-performance molecular dynamics simulations

• Epik - Rapid and robust pKa predictions

• Glide – A complete solution for ligand-receptor docking

• Impact – Molecular Dynamics Simulation

• Physical-Based ADME/Tox - Physical-Based ADME/Tox Predictions

• qpld - QM-Polarized Ligand Docking

• CovDock - An all-in-one workflow for pose prediction and scoring of covalently bound ligands

• lsdb - Ligand and Structure-Based Descriptors

• Protein Preparation Wizard - An easy-to-use tool for correcting common structural problems and creating reliable, all-atom protein models

• Induced-Fit Docking - Fast and accurate prediction of ligand induced conformational changes in receptor active sites

• Jaguar - Rapid ab initio electronic structure package

• Liaison – Predicts ligand-receptor Binding Affinity using a linear interaction approximation (LIA) model

• LigPrep - Versatile generation of accurate 3D molecular models

• MacroModel - Versatile, full-featured program for molecular modeling

• Maestro - The completely reimagined all-purpose molecular modeling environment

• Phase - An easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design

• Prime - A powerful and innovative package for accurate protein structure predictions

• QikProp - Rapid ADME predictions of drug candidates

• Qsite - A high-performance QM/MM program

• SiteMap - Fast, accurate, and practical binding site identification

中文模块介绍

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Molecular Docking Interface

• Whole operator workflow of Molecular Docking – Docking ligand to protein with SP、XS or HTVS(contain protein preparation、Ligand Preparation、Grid Generation and Docking)

  • Protein Preparation – Process Protein (contain cofactor、metal ions、water、add hydrogens、bondorder...)

  • Ligand Preparation – Process Ligand (Using epik, hydrogens、ioniztion...)

Schrödinger药物虚拟筛选流程模块 | 分子对接软件综述