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BioMedR (version 1.2.1)

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA/RNA descriptors from nucleotide sequences, and six types of interaction descriptors using three different combining strategies.

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Version

Install

install.packages('BioMedR')

Monthly Downloads

13

Version

1.2.1

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/wind22zhu/BioMedR

Maintainer

Minfeng Zhu

Last Published

July 5th, 2019

Functions in BioMedR (1.2.1)

BLOSUM100 Matrix for 20 Amino Acids

CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon

3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM50 Matrix for 20 Amino Acids

Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon

2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM45 Matrix for 20 Amino Acids

BLOSUM62 Matrix for 20 Amino Acids

BLOSUM80 Matrix for 20 Amino Acids

All 2D Descriptors for 20 Amino Acids calculated by Dragon

PAM250 Matrix for 20 Amino Acids

Information Indices Descriptors for 20 Amino Acids calculated by Dragon

BMgetDNAGenBank

Get DNA/RNA Sequences from Genbank by GI ID

Frequent Atom Pairs

cluster compounds using a descriptor database

PAM30 Matrix for 20 Amino Acids

Standard atomic weights

Jarvis-Patrick Clustering

BioMedR-package

Toolkit for Compound-Protein Interaction in Drug Discovery

Calculates the Number of Amino Acids Descriptor

2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon

Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon

Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

Topological Descriptors for 20 Amino Acids calculated by Dragon

calcParProtSeqSim

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

GETAWAY Descriptors for 20 Amino Acids calculated by Dragon

Atom pair library

Geometrical Descriptors for 20 Amino Acids calculated by Dragon

PAM120 Matrix for 20 Amino Acids

Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon

extrDrugExtendedComplete

Calculate the Extended Molecular Fingerprints (in Complete Format)

The Basic Kmer Descriptor

The Increment Of Diversity Descriptors

The Pseudo Dinucleotide Composition Descriptor

Calculate the Graph Molecular Fingerprints (in Compact Format)

Calculates All the Molecular Descriptors in the BioMedR Package at Once

Nearest Neighbors

calcParProtGOSim

Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity

Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon

A Variety of Descriptors Combining Surface Area and Partial Charge Information

3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon

calcTwoProtGOSim

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

WHIM Descriptors for 20 Amino Acids calculated by Dragon

The Trinucleotide-based Auto Covariance Descriptor

Meta Information for the 20 Amino Acids

extrPCMDescScales

Scales-Based Descriptors with 20+ classes of Molecular Descriptors

CTD Descriptors - Transition

extrPCMFAScales

Generalized Scales-Based Descriptors derived by Factor Analysis

extrPCMScaleGap

Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)

Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon

Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)

Parallellized Protein/DVA Sequence Similarity Calculation based on Sequence Alignment

extrDrugIPMolecularLearning

Calculates the Descriptor that Evaluates the Ionization Potential

extrDrugMACCSComplete

Calculate the MACCS Molecular Fingerprints (in Complete Format)

extrDrugMannholdLogP

Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms

Conjoint Triad Descriptor

extrProtCTriadClass

Conjoint Triad Descriptor (with Customized Amino Acid Classification Support)

Generalized Scales-Based Descriptors derived by Principal Components Analysis

Descriptor Characterizing the Mass Distribution of the Molecule.

Generating Interaction Descriptors

BCUT -- Eigenvalue Based Descriptor

PAM40 Matrix for 20 Amino Acids

extrProtCTDDClass

CTD Descriptors - Distribution (with Customized Amino Acid Classification Support)

extrProtCTDTClass

CTD Descriptors - Transition (with Customized Amino Acid Classification Support)

make_kmer_index

Calculate The Basic Kmer Feature Vector

Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence

extrProtPSSMAcc

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance

id_x_s function for make_kmer_vec

Protein Sequence Segmentation

Check if the DNA sequence are in the 4 default types

calcTwoProtSeqSim

Protein Sequence Alignment for Two Protein Sequences

Protein/DNA Sequence Similarity Calculation based on Gene Ontology (GO) Similarity

Read Protein Sequences in PDB Format

The Reverse chars

diversity function for make_kmer_vec

The Dinucleotide-based Auto Covariance Descriptor

Calculate the Atom Pair Fingerprints

Check if the protein sequence's amino acid types are the 20 default types

extrPCMPropScales

Generalized AA-Properties Based Scales Descriptors

extrPCMMDSScales

Generalized Scales-Based Descriptors derived by Multidimensional Scaling

extrDrugGraphComplete

Calculate the Graph Molecular Fingerprints (in Complete Format)

CTD Descriptors - Distribution

Constitutional Descriptors for 20 Amino Acids calculated by Dragon

extrDrugEstateComplete

Calculate the E-State Molecular Fingerprints (in Complete Format)

Fingerprints from descriptor vectors

Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support

Retrieve Drug Molecules in MOL and SMILES Format from Databases

Dipeptide Composition Descriptor

extrDrugHybridization

Calculate the Hybridization Molecular Fingerprints (in Compact Format)

Protein/DNA Similarity Calculation based on Gene Ontology (GO) Similarity

Quasi-Sequence-Order (QSO) Descriptor

extrDrugStandardComplete

Calculate the Standard Molecular Fingerprints (in Complete Format)

extrProtPSSMFeature

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

extrDrugStandard

Calculate the Standard Molecular Fingerprints (in Compact Format)

RDF Descriptors for 20 Amino Acids calculated by Dragon

Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization

generate statistics on sizes of clusters

PAM70 Matrix for 20 Amino Acids

AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids

OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)

Retrieve Protein Sequence in various Formats from Databases

Autocorrelation

Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges

The Pseudo K-tupler Composition Descriptor

extrDrugKappaShapeIndices

Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices

Calculate Holistic Descriptors Described by Todeschini et al.

Amino Acid Composition Descriptor

Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon

Generalized BLOSUM and PAM Matrix-Derived Descriptors

Calculate the E-State Molecular Fingerprints (in Compact Format)

Sequence-Order-Coupling Numbers

extrDrugKRComplete

Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)

Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search

2D descriptors of bcl2

visualize clustering result using multi-dimensional scaling

Calculate Drug Molecule Similarity Derived by Molecular Fingerprints

Pseudo Amino Acid Composition Descriptor

Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length

The Cross-Validation of Classification and Regression models using Partial Least Squares

Tripeptide Composition Descriptor

clusterPlotSOMmap

Plot self-organising map

Amphiphilic Pseudo Amino Acid Composition Descriptor

extrDrugHybridizationComplete

Calculate the Hybridization Molecular Fingerprints (in Complete Format)

extrDrugHybridizationRatio

Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States

extrDrugPubChemComplete

Calculate the PubChem Molecular Fingerprints (in Complete Format)

Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

The Dinucleotide-based Auto-cross Covariance Descriptor

The Trinucleotide-based Auto-cross Covariance Descriptor

Moran Autocorrelation Descriptor

Random Forest Cross-Valdidation for feature selection

Geary Autocorrelation Descriptor

Plots compound structure(s) for molecules stored in SDF and SDFset containers

The Dinucleotide-based Cross Covariance Descriptor

Calculates Atom Additive logP and Molar Refractivity Values Descriptor

extrDrugKierHallSmarts

Descriptor that Counts the Number of Occurrences of the E-State Fragments

The Trinucleotide-based Cross Covariance Descriptor

extrDrugPubChem

Calculate the PubChem Molecular Fingerprints (in Compact Format)

Read Protein/DNA Sequences in FASTA Format

The Cross-Validation of Classification and Regression models using Random Forest

extrDrugExtended

Calculate the Extended Molecular Fingerprints (in Compact Format)

extrDrugShortestPathComplete

Calculate the Shortest Path Molecular Fingerprints (in Complete Format)

CTD Descriptors - Composition

extrProtCTDCClass

CTD Descriptors - Composition (with Customized Amino Acid Classification Support)

Calculate the MACCS Molecular Fingerprints (in Compact Format)

Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List

extrProtMoreauBroto

Normalized Moreau-Broto Autocorrelation Descriptor

extrDrugShortestPath

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

Protein/DNA Sequence Alignment for Two Protein Sequences

SD file in SDFset object

Read Molecules from SDF Files and Return Parsed Java Molecular Object