Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures

Genetic algorithms in search, optimization, and machine learning

1989 • 49,726 citations

Modern Information Retrieval

1999 • 11,925 citations

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

1997 • 6,184 citations

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

1988 • 5,936 citations

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

1988 • 3,852 citations

Computer Aided Design of Experiments

1969 • 3,046 citations

Handbook of Evolutionary Computation

1997 • 3,038 citations

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1985 • 2,597 citations

Algorithm 457: finding all cliques of an undirected graph

1973 • 2,329 citations

An Algorithm for Subgraph Isomorphism

1976 • 2,189 citations

A geometric approach to macromolecule-ligand interactions

1982 • 2,146 citations

Introduction to graph theory

1997 • 1,784 citations

Chemical Similarity Searching

1998 • 1,712 citations

Mathematical Techniques in Multisensor Data Fusion

1992 • 1,379 citations

The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service.

1965 • 1,338 citations

Concepts and applications of molecular similarity

1990 • 1,312 citations

The development of versions 3 and 4 of the Cambridge Structural Database System

1991 • 1,299 citations

Readings in information retrieval

1997 • 1,103 citations

Systematic analysis of structural data as a research technique in organic chemistry

1983 • 1,035 citations

Atom pairs as molecular features in structure-activity studies: definition and applications

1985 • 952 citations

Automated docking with grid‐based energy evaluation

1992 • 911 citations

The computer program LUDI: A new method for the de novo design of enzyme inhibitors

1992 • 821 citations

Distance geometry and molecular conformation

1989 • 727 citations

Automatic text processing

1990 • 713 citations

Pharmacophore perception, development, and use in drug design

2000 • 683 citations

How similar is a molecule to another? An electron density measure of similarity between two molecular structures

1980 • 678 citations

“Scaffold-Hopping” by Topological Pharmacophore Search: A Contribution to Virtual Screening

1999 • 650 citations

Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection

1996 • 625 citations

Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited

1992 • 613 citations

The use of hierarchic clustering in information retrieval

1971 • 522 citations

An exact algorithm for the maximum clique problem

1990 • 516 citations

Automatic generation of 3D-atomic coordinates for organic molecules

1990 • 502 citations

Neighborhood Behavior: A Useful Concept for Validation of “Molecular Diversity” Descriptors

1996 • 485 citations

The graph isomorphism disease

1977 • 463 citations

Similarity and clustering in chemical information systems

1987 • 450 citations

Consensus scoring for ligand/protein interactions

2002 • 403 citations

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure

1988 • 396 citations

Why do we need so many chemical similarity search methods?

2002 • 395 citations

Multidimensional clustering algorithms

1985 • 392 citations

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

1993 • 390 citations

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

1995 • 385 citations

The theory and practice of distance geometry

1983 • 377 citations

The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding

1997 • 372 citations

Clustering and Classification

1996 • 351 citations

Implementing agglomerative hierarchic clustering algorithms for use in document retrieval

1986 • 327 citations

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

1989 • 319 citations

Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures

2004 • 315 citations

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

1999 • 312 citations

RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs

2002 • 308 citations

How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment

2001 • 300 citations

Backtrack search algorithms and the maximal common subgraph problem

1982 • 295 citations

Molecular similarity based on electrostatic potential and electric field

1987 • 293 citations

Molecular Similarity in Drug Design

1995 • 289 citations

An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap

1990 • 283 citations

Combining the evidence of multiple query representations for information retrieval

1995 • 270 citations

Chemical Similarity Using Physiochemical Property Descriptors

1996 • 261 citations

Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures

2004 • 261 citations

Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins

2002 • 254 citations

Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease.

1990 • 252 citations

Selecting Optimally Diverse Compounds from Structure Databases: A Validation Study of Two-Dimensional and Three-Dimensional Molecular Descriptors

1997 • 243 citations

Design of enzyme inhibitors using iterative protein crystallographic analysis

1991 • 228 citations

Use of techniques derived from graph theory to compare secondary structure motifs in proteins

1990 • 225 citations

3D database searching in drug design

1992 • 220 citations

A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures

1994 • 217 citations

Chemoinformatics

2003 • 205 citations

Subgraph isomorphism, matching relational structures and maximal cliques

1976 • 199 citations

Grouping of Coefficients for the Calculation of Inter-Molecular Similarity and Dissimilarity using 2D Fragment Bit-Strings

2002 • 192 citations

ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures

1989 • 188 citations

Flexible 3D searching: The directed tweak technique

1994 • 184 citations

Clustering of chemical structures on the basis of two-dimensional similarity measures

1992 • 183 citations

Substructure searching methods: Old and new

1993 • 177 citations

An introduction to chemoinformatics

2004 • 175 citations

The effectiveness of stemming for natural-language access to Slovene textual data

1992 • 173 citations

Virtual Screening for Bioactive Molecules

2000 • 169 citations

Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data

1994 • 161 citations

Algorithms and codes for the assignment problem

1988 • 161 citations

Utilization of Gaussian functions for the rapid evaluation of molecular similarity

1992 • 159 citations

Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds

1992 • 158 citations

Algorithms for the identification of three-dimensional maximal common substructures

1987 • 156 citations

An analysis of current methodologies for conformational searching of complex molecules

1988 • 149 citations

A Graph-Theoretic Algorithm for Matching Chemical Structures.

1965 • 149 citations

Three-Dimensional Pharmacophoric Pattern Searching

1977 • 149 citations

Similarity Searching Using Reduced Graphs

2003 • 148 citations

Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion

2002 • 148 citations

Molecular modeling software and methods for medicinal chemistry

1990 • 148 citations

Combinatorial Library Design Using a Multiobjective Genetic Algorithm

2002 • 148 citations

Heuristics for Similarity Searching of Chemical Graphs Using a Maximum Common Edge Subgraph Algorithm

2002 • 144 citations

Comparison of Hierarchic Agglomerative Clustering Methods for Document Retrieval

1989 • 144 citations

The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries

1997 • 142 citations

Cascade Reactions in Quantitative Solid-State Syntheses

1999 • 135 citations

Substructural analysis. Novel approach to the problem of drug design

1974 • 134 citations

A Modification of the Jaccard–Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings

2002 • 133 citations

Implementation of nearest-neighbor searching in an online chemical structure search system

1986 • 130 citations

Diversity screening versus focussed screening in drug discovery

2000 • 130 citations

CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure

1992 • 126 citations

Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties

1998 • 124 citations

The application of molecular similarity calculations

1990 • 121 citations

Stereochemically unique naming algorithm

1974 • 120 citations

Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients

2004 • 109 citations

Molecular Similarity Based on DOCK-Generated Fingerprints

1996 • 108 citations

Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases

1992 • 107 citations

Combinatorial Library Design and Evaluation

2001 • 104 citations

Similarity of molecular shape

1991 • 103 citations

Conformational freedom in 3-D databases. 1. Techniques

1990 • 101 citations

Automated site-directed drug design using molecular lattices

1992 • 100 citations

Enhancing the diversity of a corporate database using chemical database clustering and analysis

1995 • 97 citations

Distance geometry approach to rationalizing binding data

1979 • 94 citations

Computer code for producing Eh-pH plots of equilibrium chemical systems

1985 • 91 citations

Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching

1994 • 91 citations

3DSEARCH: a system for three-dimensional substructure searching

1989 • 89 citations

A fast and efficient method for 2D and 3D molecular shape description

1992 • 86 citations

Pharmacophoric pattern matching in files of 3-D chemical structures: selection of interatomic distance screens

1986 • 85 citations

Comparison of Ranking Methods for Virtual Screening in Lead-Discovery Programs

2002 • 85 citations

Searching for Patterns of Amino Acids in 3D Protein Structures

2003 • 84 citations

Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors

1999 • 83 citations

Conformation of acetylcholine bound to the nicotinic acetylcholine receptor.

1988 • 83 citations

Molecular recognition: 3D surface structure comparison by gnomonic projection

1987 • 83 citations

Pharmacophoric pattern matching in files of 3D chemical structures: comparison of geometric searching algorithms

1987 • 80 citations

Clique-Detection Algorithms for Matching Three-Dimensional Molecular Structures

1997 • 80 citations

Molecular Diversity in Drug Design

2002 • 78 citations

Shape-similarity measures for molecular bodies: A 3D topological approach to quantitative shape-activity relations

1992 • 77 citations

Structural resemblance between the families of bacterial signal-transduction proteins and of G proteins revealed by graph theoretical techniques

1990 • 75 citations

Pharmacophoric pattern matching in files of 3D chemical structures: evaluation of search performance

1987 • 75 citations

Using CONCORD to construct a large database of three-dimensional coordinates from connection tables

1989 • 74 citations

Drug Rings Database with Web Interface. A Tool for Identifying Alternative Chemical Rings in Lead Discovery Programs

2003 • 72 citations

The Hidden Component of Size in Two-Dimensional Fragment Descriptors: Side Effects on Sampling in Bioactive Libraries

1999 • 72 citations

Molecular recognition: optimized searching through rotational 3-space for pattern matches on molecular surfaces

1987 • 72 citations

Automated site-directed drug design: the concept of spacer skeletons for primary structure generation

1989 • 72 citations

Automated site-directed drug design : the formation of molecular templates in primary structure generation

1989 • 70 citations

Evaluation of a novel infrared range vibration-based descriptor (EVA) for QSAR studies. 1. General application.

1997 • 69 citations

Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets

1999 • 67 citations

Automatic search for maximum similarity between molecular electrostatic potential distributions

1991 • 67 citations

Computer-assisted examination of compounds for common three-dimensional substructures

1983 • 67 citations

Further annotated bibliography on the isomorphism disease

1979 • 67 citations

Evolutionary Algorithms in Molecular Design

2000 • 65 citations

Quantitative comparison of molecular electrostatic potentials for structure‐activity studies

1991 • 64 citations

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances

1991 • 62 citations

Sequence-dependent DNA Structure: A Database of Octamer Structural Parameters

2003 • 62 citations

Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules

1990 • 62 citations

Computer‐Assisted Molecular Design (CAMD)—An Overview

1987 • 61 citations

Molecular recognition: blindsearching for regions of strong structural match on the surfaces of two dissimilar molecules

1988 • 59 citations

Searching for pharmacophores in large coordinate data bases and its use in drug design.

1989 • 58 citations

Similarity searching on CAS Registry substances. 1. Global molecular property and generic atom triangle geometric searching

1992 • 58 citations

A review and examination of the mathematical spaces underlying molecular similarity analysis

1989 • 58 citations

Automated conformational analysis: Directed conformational search using the A* algorithm

1990 • 58 citations

NMR studies of molecular complexes as a tool in drug design

1991 • 57 citations

DIVSEL and COMPLIB - Strategies for the Design and Comparison of Combinatorial Libraries using Pharmacophoric Descriptors

1998 • 57 citations

An Efficient Implementation of Distance-Based Diversity Measures Based on k−d Trees

1998 • 56 citations

DARC substructure search system: a new approach to chemical information

1983 • 56 citations

Dopamine agonists: structure-activity relationships

1985 • 56 citations

A method for the automatic classification of chemical structures

1973 • 55 citations

IcePick: A Flexible Surface-Based System for Molecular Diversity

1998 • 55 citations

OVID and SUPER: Two overlap programs for drug design

1991 • 55 citations

Computer storage and retrieval of generic chemical structures in patents. 7. Parallel simulation of a relaxation algorithm for chemical substructure search

1986 • 53 citations

Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads

1991 • 52 citations

Computer-aided interpretation of mass spectra. 20. Molecular structure comparison program for the identification of maximal common substructures

1977 • 52 citations

Automated site-directed drug design : the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces

1989 • 51 citations

The Automatic Detection of Chemical Reaction Sites

1978 • 51 citations

Similarity searching in databases of three-dimensional molecules and macromolecules

1992 • 49 citations

Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem

1991 • 48 citations

Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of bounded distance matrices for the representation and searching of conformationally flexible molecules

1992 • 48 citations

Data base development and search algorithms for automated infrared spectral identification

1985 • 48 citations

Three‐dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph‐theoretical techniques

1992 • 45 citations

Automated site-directed drug design: Approaches to the formation of 3D molecular graphs

1990 • 44 citations

The search for functional correspondences in molecular structure between two dissimilar molecules

1985 • 43 citations

An integrated approach to three-dimensional information management with MACCS-3D

1991 • 42 citations

The Sheffield Generic Structures Projecta Retrospective Review

1996 • 42 citations

Substructure Search by Set Reduction

1972 • 42 citations

Virtual Screening: An Alternative or Complement to High Throughput Screening?

2002 • 42 citations

New Diversity Calculations Algorithms Used for Compound Selection

2002 • 42 citations

Automated structure design in 3D

1990 • 41 citations

Carbon-13 nuclear magnetic resonance spectral interpretation by a computerized substituent chemical shift method

1983 • 41 citations

Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs.

1997 • 41 citations

Algorithm5: A Technique for Fuzzy Similarity Clustering of Chemical Inventories

1996 • 40 citations

Comparison of protein surfaces using a genetic algorithm.

1997 • 40 citations

Automatic superposition of drug molecules based on their common receptor site

1992 • 40 citations

Computer-Assisted Examination of Chemical Compounds for Structural Similarities

1979 • 39 citations

An Efficient Design for Chemical Structure Searching. I. The Screens

1975 • 39 citations

WIZARD: applications of expert system techniques to conformational analysis. 1. The basic algorithms exemplified on simple hydrocarbons

1987 • 38 citations

Use of flexible queries for searching conformationally flexible molecules in databases of three-dimensional structures

1992 • 38 citations

The Chemical Abstracts Service Chemical Registry System. II. Augmented Connectivity Molecular Formula

1979 • 36 citations

Selection of Descriptors According to Discrimination and Redundancy. Application to Chemical Structure Searching

1976 • 34 citations

3D Database searching on the basis of ligand shape using the sperm prototype method

1990 • 34 citations

Computational experience with an algorithm for tetrangle inequality bound smoothing

1989 • 33 citations

A fast procedure for the calculation of similarity coefficients in automatic classification

1981 • 33 citations

A Method of Cluster Analysis and Some Applications

1968 • 33 citations

3D database searching and de novo construction methods in molecular design

1990 • 32 citations

The application of Artificial Intelligence to the conformational analysis of strained molecules

1990 • 32 citations

AIMB: Analogy and intelligence in model building. System description and performance characteristics

1988 • 31 citations

Hash Functions for Rapid Storage and Retrieval of Chemical Structures

1978 • 31 citations

Graph theoretic methods for the analysis of structural relationships in biological macromolecules

2005 • 30 citations

The discovery of novel auxin transport inhibitors by molecular modeling and three-dimensional pattern analysis

1991 • 30 citations

Expert system for machine-aided indexing

1987 • 30 citations

The Centroid Approximation for Mixtures: Calculating Similarity and Deriving Structure−Activity Relationships

2000 • 30 citations

Vertex indexes of molecular graphs in structure-activity relationships: a study of the convulsant-anticonvulsant activity of barbiturates and the carcinogenicity of unsubstituted polycyclic aromatic hydrocarbons

1990 • 29 citations

A rapid method for comparing and matching the spherical parameter surfaces of molecules and other irregular objects

1989 • 29 citations

Selection of screens for three-dimensional substructure searching

1990 • 29 citations

Using three-dimensional substructure searching to identify novel, non-peptidic inhibitors of HIV-1 protease

1990 • 28 citations

Draft specification for revised version of the Standard Molecular Data (SMD) Format

1990 • 28 citations

Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures

1990 • 28 citations

Compare Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles

1992 • 28 citations

Identification of .beta.-sheet motifs, of .psi.-loops, and of patterns of amino acid residues in three-dimensional protein structures using a subgraph-isomorphism algorithm

1994 • 28 citations

Similarity Searching in Databases of Flexible 3D Structures Using Smoothed Bounded Distance Matrices

2003 • 26 citations

A Screen Set Generation Algorithm

1979 • 26 citations

Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems

1990 • 26 citations

Computerized selection of potential DNA binding compounds.

1990 • 26 citations

Rapid geometric searching in protein structures

1989 • 25 citations

Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly

1992 • 25 citations

MCSS: a new algorithm for perception of maximal common substructures and its application to NMR spectral studies. 1. The algorithm

1992 • 25 citations

Automated site-directed drug design: a method for the generation of general three-dimensional molecular graphs

1992 • 24 citations

Molecular structure matching by simulated annealing. IV. Classification of atom correspondences in sets of dissimilar molecules

1991 • 24 citations

Sequence−Structure Relationships in DNA Oligomers: A Computational Approach

2001 • 24 citations

GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1

2003 • 23 citations

Transputer implementations of chemical substructure searching algorithms

1988 • 22 citations

Bibliographic pattern matching using the ICL Distributed Array Processor

1988 • 21 citations

Computer design of potentially bioactive molecules by geometric searching with ALADDIN

1990 • 21 citations

Deriving three-dimensional representations of molecular structure from connection tables augmented with configuration designations using distance geometry

1982 • 20 citations

New 3-D Search and De Novo Design Techniques Aid Drug Development

1992 • 20 citations

Looking for pharmacophores in 3-D databases: Does conformational searching improve the yield of actives?

1990 • 20 citations

A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching.

2000 • 19 citations

Pharmacophoric pattern matching in files of three-dimensional chemical structures: Characterization and use of generalized valence angle screens

1991 • 19 citations

A polymerase I palm in adenylyl cyclase?

1997 • 19 citations

Characteristics of computer-generated 3D and related molecular property data for CAS registry substances

1990 • 19 citations

Status and future developments of reaction databases and online retrieval systems

1990 • 18 citations

A review of three‐dimensional chemical structure retrieval systems

1992 • 18 citations

Representation and searching of carbohydrate structures using graph-theoretic techniques

1997 • 18 citations

Remark on Algorithm 323: Generation of Permutations in Lexicographic Order [G6]

1973 • 17 citations

Electronically Controlled Respirator

1957 • 17 citations

Database structure and searching in MACCS-3D

1990 • 17 citations

The standard molecular data format (SMD format) as an integration tool in computer chemistry

1989 • 17 citations

The Evaluation of an Automatically Indexed, Machine-Readable Chemical Reactions File

1980 • 16 citations

Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments

1992 • 16 citations

A Structural Similarity Analysis of Double-helical DNA

2004 • 16 citations

Molecular Dissimilarity in Chemical Information Systems

1993 • 16 citations

Network design for the implementation of text searching using a multicomputer

1991 • 16 citations

Conformational analysis and computer graphics in drug research

1988 • 16 citations

Computer storage and retrieval of generic chemical structures in patents. 11. Theoretical aspects of the use of structure languages in a retrieval system

1991 • 15 citations

Biologically active phenolics from Lilium longiflorum

1981 • 15 citations

Development of an atom mapping procedure for similarity searching in databases of three‐dimensional chemical structures

1991 • 15 citations

Substructure search systems for large chemical data bases

1990 • 15 citations

Evaluation and implementation of topological codes for online compound search and registration

1981 • 15 citations

Phytotropins: Conformational requirements for the abolition of the root geotropic response

1981 • 13 citations

A Representation of π Systems for Efficient Computer Manipulation

1979 • 13 citations

Substructure Search on Very Large Files Using Tree-Structured Databases

1988 • 13 citations

Automated site-directed drug design: Searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly

1992 • 13 citations

DOCKing ligands into receptors: The test case of α-chymotrypsin

1990 • 13 citations

Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of smoothed bounded distances for incompletely specified query patterns

1991 • 13 citations

Some heuristics for nearest-neighbor searching in chemical structure files

1983 • 13 citations

Building 3D structural databases: Experiences with MDDR-3D and FCD-3D

1990 • 13 citations

Use of molecular fields to compare series of potentially bioactive molecules designed by scientists or by computer

1990 • 12 citations

Analysis of structural characteristics of chemical compounds in a large computer-based file. Part III. Statistical association of fragment incidence

1972 • 11 citations

Experiences building and searching the Chapman & Hall Dictionary of Drugs

1990 • 10 citations

Relationship between Query and Data-Base Microstructure in General Substructure Search Systems

1973 • 8 citations

Errata

1986 • 7 citations

A Qualitative Comparison of Wiswesser Line Notation Descriptors of Reactions and the Derwent Chemical Reaction Documentation Service

1979 • 6 citations

Production of Printed Indexes of Chemical Reactions. I. Analysis of Functional Group Interconversions

1973 • 5 citations

An Integrated Approach to 2-D and 3-D Similarity Searching for the Cambridge Structural Database (CSD)

1993 • 2 citations