- Table of Contents
- 1. Overview
- 1.1. What is VolSurf+?
- 1.2. Program citation
- 1.3. Program organization
- 1.4. Limitations
- 2. What is new in VolSurf+?
- 2.1. New Modules in VolSurf+
- 2.2. New descriptors
- 2.3. Standard library models
- 2.4. Automatic Protonation-Deprotonation
- 2.5. Handling of SMILES structure or 2D SD files
- 2.6. Handling of a large series of compounds
- 2.7. User settings
- 2.8. Independence from the operating system
- 2.9. New and more flexible command line interface
- 3. Installation
- 4. Background
- 5. VolSurf+ Descriptors
- 5.1. Overview
- 5.2. Details
- 5.2.1. Size and shape descriptors
- 5.2.2. Descriptors of hydrophilic regions
- 5.2.3. Descriptors of hydrophobic regions
- 5.2.4. INTEraction enerGY (= INTEGY) moments
- 5.2.5. Descriptors of H-bond donor / acceptor regions
- 5.2.6. Mixed descriptors
- 5.2.7. Charge State descriptors
- 5.2.8. 3D pharmacophoric descriptors
- 5.2.9. ADME model descriptors
- 5.3. Conclusions
- 6. VolSurf+ ADME descriptors
- 7. Statistical Tools
- 7.1. Principal Components Analysis (PCA)
- 7.1.1. Uses of PCA
- 7.2. Consensus PCA
- 7.2.1. Uses of CPCA
- 7.3. Partial Least Squares (PLS)
- 7.3.1. PLS modeling
- 7.3.2. Tests of predictive ability: Cross-validation
- 7.3.3. Uses of PLS
- 7.4. References
- 8. Modeling data
- 9. Command-line interface
- 9.1. Introduction
- 9.2. Keywords
- 9.2.1. General keywords
- 9.2.2. Constants (VSL_constant)
- 9.2.3. Parameters (VSL_param)
- 9.3. Strings (VSL_string)
- 9.4. VSL statements
- 9.4.1. File statements
- 9.4.2. Import statements
- 9.4.3. Datamatrix Export statements
- 9.4.4. Configure statements
- 9.4.5. Modeling statements
- 9.4.6. Selector statements
- 10. Overview of the program GRID
- 10.1. Energy functions of program GRID
- 10.1.1. The Lennard-Jones potential
- 10.1.2. The electrostatic potential
- 10.1.3. The hydrogen bond potential
- 10.1.4. The entropy term
- 10.2. VolSurf+ Probes
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