]> Descriptor Ontology 210 2009-07-19 Category Algorithm Descriptor A feature (descriptor) is an algorithm that operates on a chemical entity (commonly atoms and molecules) and returns a numerical or nominal (descriptor) value which described certain information on that entity. Atomic Descriptors 2005-11-18 Atomic Descriptors 2009-07-07 Molecular Descriptors 2005-11-18 Protein Descriptor 2006-11-02 A descriptor specifically designed for characterizing proteins Contributor Data Feature Data Representation Implementation Descriptor Value One or more output values calculated by an Implementation of a certain Algorithm for a certain molecule. Is A Instance Of Is Classified As Requires has 2D Coordinates has 3D Coordinates has Fractional Unit Cell Coordinates Coordinates has Partial Atomic Charges Dietz Representation Graph Representation Representation in which atoms are represented by graph nodes and bonds by graph edges. Consequently, bonds are always localized between two atoms. Joerg Kurt Wegner Egon Willighagen Peter Murray-Rust Christian Hoppe Rajarshi Guha Todd Martin Matteo Floris Miguel Rojas Federico Marighetti DescriptorCategories 2005-11-18 Electronic Descriptors 2005-02-07 Descriptor relating to the electronic distribution in a molecule. Constitutional Descriptor 2005-02-07 Descriptor reflecting the molecular composition of a compound without connectivity and geometry information. Geometrical Descriptor 2005-02-07 Any descriptor derived from the three-dimensional structure of the molecule. Hybrid Descriptor Topological Descriptor 2005-02-07 Descriptor reflecting the molecular connectivity without geometry information. Amino Acid Count 2006-01-15 Returns the number of amino acids found in the system Atomic Polarizabilities 2004-11-26 Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens). Polarizabilities derive from periodic tables. Element Count 2004-11-26 Descriptor based on the number of atoms of a certain element type. Atomic Degree 2004-11-26 Descriptor that calculates the number of not-Hs substituents of an atom. Atomic Hybridization 2004-11-26 Descriptor that returns the hybridization state of an atom. Atomic Hybridization VSEPR 2006-05-08 Descriptor that returns the hybridization state of an atom. The calculation find a SIMPLE WAY the molecular geometry for following from Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its hybridization of atoms in a molecule. Atomic Valence 2004-11-26 Descriptor that calculates the valence of an atom. Aromatic Atoms Count 2004-11-26 Descriptor based on the number of aromatic atoms of a molecule. Aromatic Bonds Count 2004-11-26 Descriptor based on the number of aromatic bonds of a molecule. Inductive atomic hardness 2005-04-21 This class calculates the atomic hardness of a given atom. Inductive atomic hardness of an atom in a polyatomic system can be defined as the resistance to a change of the atomic charge. This descriptor is described by Cherkasov . Inductive atomic softness 2005-04-21 This class calculates the atomic softness of a given atom. Inductive atomic softness of an atom in a polyatomic system can be defined as as charge delocalizing ability. This descriptor is described by Cherkasov . BCUT 2005-01-27 Eigenvalue based descriptor noted for its utility in chemical diversity described by Pearlman et al. . Bond Count 2004-11-26 Descriptor based on the number of bonds of a certain bond order. Bonds to Atom 2004-11-26 Descriptor based on the number of bonds on the shortest path between two atoms. Bond Polarizabilities 2004-11-26 Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens). Polarizabilities derive from periodic tables. Valence connectivity index (order 1) 2004-11-26 Descriptor that calculates atomic valence connectivity index (order 1). Let v i = ( v i - h i ) ( z i - h i - 1 ) , where p i is the numbers of valence electrons of atom i, h i is the number of hydrogens bonded to atom i, and z i is the atomic number of atom i. Valence connectivity is calculated as the sum of 1 ( v i v j ) 0.5 over all bonds between heavy atoms i and j. Valence carbon connectivity index (order 1) 2004-11-26 Descriptor that calculates carbon valence connectivity index (order 1). Let v i = ( v i - h i ) ( z i - h i - 1 ) , where p i is the numbers of valence electrons of atom i, h i is the number of hydrogens bonded to atom i, and z i is the atomic number of atom i. While the valence connectivity is calculated as the sum of 1 ( v i v j ) 0.5 over all bonds between heavy atoms i and j, the carbon valence connectivity index takes into account only bonds between carbon atoms. Valence connectivity index (order 0) 2004-11-26 Descriptor that calculates atomic valence connectivity index (order 0). Let v i = ( v i - h i ) ( z i - h i - 1 ) , where p i is the numbers of valence electrons of atom i, h i is the number of hydrogens bonded to atom i, and z i is the atomic number of atom i. Valence connectivity is calculated as the sum of 1 ( v i ) 0.5 over all heavy atoms i with v i greather than 0. Valence carbon connectivity index (order 0) 2004-11-26 Descriptor that calculates carbon valence connectivity index (order 0). Let v i = ( v i - h i ) ( z i - h i - 1 ) , where p i is the numbers of valence electrons of atom i, h i is the number of hydrogens bonded to atom i, and z i is the atomic number of atom i. While the atomic valence connectivity is calculated as the sum of 1 ( v i ) 0.5 over all heavy atoms i with v i greather than 0, the carbon valence connectivity index takes into account only carbon atoms with v i greather than 0. Carbon connectivity index (order 0) 2004-11-26 Descriptor that calculates the carbon connectivity index (order 0). While the atomic connectivity is calculated as the sum of 1 d i 0.5 over all heavy atoms i with degree greather than zero, carbon connectivity index takes into account only carbon atoms with degree greather than zero. Carbon connectivity index (order 1) 2004-11-26 Descriptor that calculates carbon connectivity index (order 1). While the atomic connectivity is calculated as the sum of 1 ( d i d j ) 0.5 over all bonds between heavy atoms i and j, the carbon connectivity index takes into account only bonds between carbon atoms. Distance to Atom 2004-11-26 Descriptor that calculates the 3D distance between two atoms. Effective Polarizability 2004-11-26 Descriptor that calculates the effective polarizability of a given heavy atom. Polarizabilities are assigned to the heavy atom by Polarizability class. Gravitational Index 2004-11-24 Descriptor characterizing the mass distribution of the molecule. This descriptor is described by Katritzky et al. . Gravitational Index (Square and Cube Roots) 2004-11-25 Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index. This descriptor is described by Wessel et al. . Hydrogen Bond Acceptors 2004-11-26 Descriptor that calculates the number of hydrogen bond acceptors. Hydrogen Bond Donors 2004-11-26 Descriptor that calculates the number of hydrogen bond donors. Hydrogen Bond Acceptors (Daylight) 2004-11-26 Descriptor that calculates the number of hydrogen bond acceptors. As defined by Daylight website, , a H-bond acceptor is a heteroatom with no positive charge, note that negatively charged oxygen or sulphur are included. Excluded are halogens, including F, heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded. Note P(III) is currently included. Zeneca's work would imply that (O=S=O) shoud also be excluded. Hydrogen Bond Donors (Daylight) 2004-11-26 Descriptor that calculates the number of hydrogen bond donors. As defined by Daylight website, , a H-bond acceptor must have an N-H bond, an O-H bond, or a F-H bond Acceptor Field Atoms (Boehm,Klebe) 2006-09-08 Counts the number of acceptor field atoms for a carbonyl oxygen probe. Force field based definition of hydrogen bond acceptors This rule covers nitril, carbonyl, ether, and amin nitrogens. Donor Field Atoms (Boehm,Klebe) 2006-09-08 Counts the number of donor field atoms for an amino hydrogen probe. Force field based definition of hydrogen bond donors . This rule covers amino groups, chloro, bromo and iodo atoms . Acceptors or Donors Field Atoms (Boehm,Klebe) 2006-09-08 Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe. Force field based definition of hydrogen bond acceptors or donors . This rule covers amino and hydroxy groups. Proton belonging to an aromatic system 2005-01-27 This Class contains a method that returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and 0 for other positions. Proton belonging to a pi-system 2005-01-27 This Class contains a method that returns true if the protons is directly bonded to a pi system. Kier and Hall kappa molecular shape indices 2004-11-26 Descriptor that calculates Kier and Hall kappa molecular shape indices. Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs. First kappa shape index is given by n ( n - 1 ) 2 m 2 , second kappa shape index is given by ( n - 1 ) ( n - 2 ) 2 p 2 2 and third kappa shape index is given by ( n - 1 ) ( n - 3 ) 2 p 3 2 for odd n and ( n - 3 ) ( n - 2 ) 2 p 3 2 for enev n, where n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3 Largest Chain 2005-02-07 Returns the number of atoms in the largest chain Largest Pi Chain 2005-02-07 Returns the number of atoms in the largest pi chain Lipinski's Rule of Five 2005-01-27 This Class contains a method that returns the number failures of the Lipinski's Rule Of Five. The Rule of 5 got its name from the cutoff values for each of the four parameters that define the potential of a drug candidate for good absorption: all of these values are close to five or a multiple of five. The original definition, given by Christopher A. Lipinski, says that poor absorption (or permeation) is more likely when: the molecule has more than 5 H-bond donors and more than 10 H-bond acceptors; its molecular weight is over 500. its LogP is over 5; Longest Aliphatic Chain 2005-02-07 Returns the number of atoms in the longest aliphatic chain Moments of Inertia 2005-02-07 Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration. Partial Pi Charge 2006-05-08 Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom. Calculation is based on Gasteiger H.Saller (PEPE) . Partial Pi Charge 2006-05-08 Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom. Calculation is based on Gasteiger Marsili (PEOE) . Partial Total Charge (MMFF94) 2006-05-08 Descriptor that calculates total partial charges of an heavy atom. Calculation is based on MMFF94. Period of an atom 2005-02-07 Descriptor that returns the period in the periodic table of an atom belonging to an atom container Petitjean Number 2005-02-07 Descriptor that calculates the Petitjean Number of a molecule. According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph. The distance is obtained from the distance matrix as the count of edges between the two vertices. If r i is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r i . The graph diameter D is defined as the largest vertex eccentricity in the graph. Petitjean Number is the value of ( diameter - radius ) diameter . Pi-contact of two atoms 2005-02-07 Descriptor that check if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighboors of the atoms). Pi Electronegativity 2006-05-08 This algorithm contains a method that returns the pi electronegativity for a given atom. Pi electronegativity is given by X = a + b q + c ( q 2 ) , where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge. Proton Total Partial Charge 2005-02-07 Descriptor that calculates partial charges of an heavy atom and its protons. Calculation is based on Gasteiger Marsili (PEOE) RDF Proton Descriptor 2005-01-27 Calculation of RDF proton descriptor based on . A given proton is represented by 5 different descriptors. The first one has the form g H r p i e - B ( r - r i ) 2 where i denotes an atom up to four not rotatable bonds away from the target proton, p is the partial atomic charge of the atom i, B is a smoothing parameter, r i is the 3D distance between proton and atom i, and r is a running variable. The second one is a topological form of the first one, where i is an atom up to the fifth sphere, p i is the partial atomic charge of atom i, and r i is now the sum of bond length on the shortest path between the proton and atom i. The third one has the form g D r 1 r D,i 2 e - B ( r - a D,i ) 2 where i denotes a double bond up to the seventh sphere of nonrotatable bonds centered on the target proton, and r D and a D are geometric variables. The fourth one has the form g S r 1 r S,i 2 e - B ( r - a S,i ) 2 where i denotes a single bond up to the seventh sphere of nonrotatable bonds centered on the target proton, and r S and a S are geometric variables. The last one has the form g 3 r e - B ( r - a 3,i ) 2 where i denotes an atom three nonrotatable bonds away from the target proton and belonging to a six-membered ring, and a 3 is a dihedral angle in radian units. Each values is returned as atom property. Rotatable Bonds Count 2005-02-07 Descriptor that calculates the number of nonrotatable bonds on a molecule. The number of rotatable bonds is given by the SMARTS specified by Daylight on . Sigma Electronegativity 2005-02-07 This Class contains a method that returns the sigma electronegativity for a given atom. Sigma electronegativity is given by X = a + b q + c ( q 2 ) , where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge. Topological Polar Surface Area 2005-01-27 Calculation of topological polar surface area based on fragment contributions . Molecular Weight 2005-01-27 Descriptor based on the weight of atoms of a certain element type. If no element is specified, the returned value is the Molecular Weight WHIM 2005-01-27 Holistic descriptors described by Todeschini et al . Wiener Numbers 2005-01-27 This class calculates Wiener path number and Wiener polarity number. Wiener path number: half the sum of all the distance matrix entries. Wiener polarity number: half the sum of all the distance matrix entries with a value of 3. Vertex adjacency information magnitude 2004-11-26 Descriptor that calculates the vertex adjacency information of a molecule. The values is given by 1 + log 2 * m , where m is the number of heavy-heavy bonds. If m is zero, then zero is returned. Van der Waals radius 2005-01-27 Descriptor that returns the VdW radius of a given atom. XLogP 2005-01-27 Prediction of logP based on the atom-type method called XLogP. For a description of the methodology see . ALogP 2005-01-27 Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen and Zagreb Index 2004-11-26 The sum of the squared atom degrees of all heavy atoms. Covalent Radius 2006-05-08 Descriptor that returns the covalent radius of a given atom. Bond Partial Pi Charge 2006-05-08 Descriptor that calculates bond-pi Partial charge of a bond. Calculation is calculated determining the difference the Partial Pi Charge on atoms A and B of a bond. Based in Gasteiger Charge. Bond Partial Sigma Charge 2006-05-08 Descriptor that calculates bond-sigma Partial charge of a bond. Calculation is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond. Based in Gasteiger Charge. Bond Partial Total Charge 2006-05-08 Descriptor that calculates bond-total Partial charge of a bond. Calculation is calculated determining the difference the Partial Total Charge on atoms A and B of a bond. Based in Gasteiger Charge. Bond Sigma Electronegativity 2006-05-08 Descriptor that calculates of bond-Polarizability of a bond. Calculation is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond. Petitjean Shape Indices 2006-01-15 The topological and geometric shape indices described Petitjean and Bath et al. respectively. Both measure the anisotropy in a molecule. Ring Count 2009-07-23 Descriptor that counts the number of rings in the molecules. Optionally, it counts the number rings with a specified number of ring atoms. Eccentric Connectivity Index 2005-03-19 A topological descriptor combining distance and adjacency information. The eccentric connectivity index for a hydrogen supressed molecular graph is given by the expression $${\xi }^c=\sum _{i=1}nE\left(i\right)V\left(i\right)$$ where E(i) is the eccentricity of the i ^th atom (path length from the i ^th atom to the atom farthest from it) and V(i) is the vertex degree of the i ^th atom. Charged Partial Surface Areas 2005-05-16 A variety of descriptors combining surface area and partial charge information Fragment Complexity 2006-8-22 Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06} Weighted path descriptors 2006-01-15 The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching. Moreau-Broto Autocorrelation (charge) descriptors 2006-01-15 The Moreau-Broto autocorrelation descriptors using partial charges Moreau-Broto Autocorrelation (polarizability) descriptors 2006-01-15 The Moreau-Broto autocorrelation descriptors using polarizability Moreau-Broto Autocorrelation (mass) descriptors 2006-01-15 The Moreau-Broto autocorrelation descriptors using atomic weight TAE RECON descriptors for amino acid sequences 2006-08-23 The TAE RECON descriptors for amino acid sequences. Uses precalculated quantum mechanical parameters to generate a set of 147 descriptors for a given sequence Molecular Distance Edge 2006-09-18 Evaluate molecular distance edge descriptors for C, N and O For a description of the methodology see . Length Over Breadth 2006-09-26 Calculates the ratio of length to breadth. The descriptor has two values indicating the maximum and minimumn value of LoB. Note that this method does not perform any orientation. Chi Chain Indices 2006-11-12 Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6 Both the simple and valence versions of this descriptor are evaluated Chi Path Indices 2006-11-12 Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7 Both the simple and valence versions of this descriptor are evaluated Chi Cluster Indices 2006-11-13 Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7 Both the simple and valence versions of this descriptor are evaluated Chi Path-Cluster Indices 2006-11-13 Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6 Both the simple and valence versions of this descriptor are evaluated Carbon Types 2006-09-26 Characterizes the carbon connectivity in terms of hybridization This is a port of the ADAPT CTYPES routine and is a count of carbon atom in different hybridization states and environments Kier & Hall SMARTS 2006-09-26 Counts the number of occurrences of the E-state fragments Traditionally, the E-state indices are obtained by identifying a set of fragments and then evaluating the E-state index from them. However it has been shown by Butina (Molecules, 2004, 9, 1004-1009) that the frequency of occurrence of the fragments can lead to QSAR models that perform as well as those based on the original E-state indices. This descriptor generates counts for 35 fragments. Descriptor names are prefixed with "khs." Ionization Potential 2006-01-15 Descriptor that evaluates the ionization potential. It should be noted that the descriptor values are obtained using a predictive model and are not calculated directly from the structure Bath, P.A. and Poirette, A.R. and Willet, P. and Allen, F.H. The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape Coefficients of Chemical Compounds Journal of Chemical Information and Computer Science 1995 35 714-716 Böhm, M. and Klebe, G. Development of New Hydrogen-Bond Descriptors and Their {A}pplication to Comparative Molecular Field Analyses J. Med. Chem. 2002 45 1585-1597 Cherkasov, A. Inductive Electronegativity Scale. 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On molecular identification numbers Journal of Chemical Information and Computer Science 1984 24 164-175 Gasteiger, J. Saller, H. Berechnung der Ladungsverteilung in konjugierten Systemen durch eine Quantifizierung des Mesomeriekonzeptes Angew. Chem. 1985 97 699-701 Todeschini, R. and Consonni, V. Handbook of Molecular Descriptors 2000 3-52-29913-0 Todeschini, R. and Gramatica, P. New 3D Molecular Descriptors: The WHIM theory and QAR Applications Persepectives in Drug Discovery and Design 1998 355-380 Trinijastic, N. Chemical Graph Theory CRC Press 1992 0-8493-4256-2 Wang, R., Fu, Y., and Lai, L. A New Atom-Additive Method for Calculating Partition Coefficients Journal of Chemical Information and Computer Sciences 1997 37 615-621 Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M. Prediction of Human Intestinal Absorption of Drug Compounds From Molecular Structure Journal of Chemical Information and Computer Sciences 1998 38 726-735