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Journal of Chemical Information and Modeling, Volume 46
Volume 46, Number 1, January 2006
- Dilip K. Sinha, Subhash C. Basak:
Fourth Indo-U.S. Workshop on Mathematical Chemistry, January 8-12, 2005, Pune, Maharashtra, India. 1 - Matevz Pompe, Milan Randic:
"Anticonnectivity": A Challenge for Structure-Property-Activity Studies. 2-8 - Douglas M. Hawkins, Subhash C. Basak, Jessica J. Kraker, Kevin T. Geiss, Frank A. Witzmann:
Combining Chemodescriptors and Biodescriptors in Quantitative Structure-Activity Relationship Modeling. 9-16 - Om Prakash Pandey, Indira Ghosh:
Developing an Antituberculosis Compounds Database and Data Mining in the Search of a Motif Responsible for the Activity of a Diverse Class of Antituberculosis Agents. 17-23 - Subhash Ajmani, Kamalakar Jadhav, Sudhir A. Kulkarni:
Three-Dimensional QSAR Using the k-Nearest Neighbor Method and Its Interpretation. 24-31 - Marco Pintore, Christophe Wechman, Gilles Sicard, Maurice Chastrette, Nicolas Amaury, Jacques R. Chrétien:
Comparing the Information Content of Two Large Olfactory Databases. 32-38 - Philip Prathipati
, Anil K. Saxena:
Evaluation of Binary QSAR Models Derived from LUDI and MOE Scoring Functions for Structure Based Virtual Screening. 39-51 - Yenamandra S. Prabhakar
, Krishnan Balasubramanian:
A Simple Algorithm for Unique Representation of Chemical Structures-Cyclic/Acyclic Functionalized Achiral Molecules. 52-56 - Milan Randic, Alexandru T. Balaban:
Partitioning of pi-Electrons in Rings for Clar Structures of Benzenoid Hydrocarbons. 57-64 - Subhash C. Basak, Ramanathan Natarajan
, Denise R. Mills, Douglas M. Hawkins, Jessica J. Kraker:
Quantitative Structure-Activity Relationship Modeling of Juvenile Hormone Mimetic Compounds for Culex Pipiens Larvae, with a Discussion of Descriptor-Thinning Methods. 65-77 - Samrat Dutta, Poonam Singhal, Praveen Agrawal, Raju Tomer, Kritee, Ekta Khurana, Bhyravabhotla Jayaram
:
A Physicochemical Model for Analyzing DNA Sequences. 78-85 - Yenamandra S. Prabhakar
, Manish K. Gupta, Nobendu Roy, Yenamandra Venkateswarlu:
A High Dimensional QSAR Study on the Aldose Reductase Inhibitory Activity of Some Flavones: Topological Descriptors in Modeling the Activity. 86-92 - Manish K. Gupta, Yenamandra S. Prabhakar
:
Topological Descriptors in Modeling the Antimalarial Activity of 4-(3', 5'-Disubstituted anilino)quinolines. 93-102 - Mamta Thakur
, Abhilash Thakur, Krishnan Balasubramanian:
QSAR and SAR Studies on the Reduction of Some Aromatic Nitro Compounds by Xanthine Oxidase. 103-110 - Akbar S. Khan, Cesar V. Mujer, Timothy G. Alefantis, Joseph P. Connolly, Ulrike Beate Mayr, Petra Walcher, Werner Lubitz, Vito G. DelVecchio:
Proteomics and Bioinformatics Strategies to Design Countermeasures against Infectious Threat Agents. 111-115 - Milan Randic, Frank A. Witzmann, Varshna Kodali, Subhash C. Basak:
On the Dependence of a Characterization of Proteomics Maps on the Number of Protein Spots Considered. 116-122 - R. Sathyapriya, K. V. Brinda, Saraswathi Vishveshwara:
Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures. 123-129 - Marjan Vracko, Subhash C. Basak, Kevin T. Geiss, Frank A. Witzmann:
Proteomic Maps-Toxicity Relationship of Halocarbons Studied with Similarity Index and Genetic Algorithm. 130-136
- Yun-De Xiao, Rebecca Harris, Ersin Bayram, Peter Santago II, Jeffrey D. Schmitt:
Supervised Self-Organizing Maps in Drug Discovery. 2. Improvements in Descriptor Selection and Model Validation. 137-144 - Gemma L. Holliday
, Peter Murray-Rust, Henry S. Rzepa:
Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions. 145-157 - Zsolt Lepp, Takashi Kinoshita
, Hiroshi Chuman:
Screening for New Antidepressant Leads of Multiple Activities by Support Vector Machines. 158-167 - Anna Maria Almerico
, Marco Tutone
, Antonino Lauria
, Patrizia Diana, Paola Barraja
, Alessandra Montalbano, Girolamo Cirrincione, Gaetano Dattolo:
A Multivariate Analysis of HIV-1 Protease Inhibitors and Resistance Induced by Mutation. 168-179 - Robert P. Sheridan, Peter Hunt, J. Christopher Culberson:
Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR. 180-192 - Meir Glick, Jeremy L. Jenkins
, James H. Nettles, Hamilton Hitchings, John W. Davies:
Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers. 193-200 - Andrew Smellie, Christopher J. Wilson, Shi Chung Ng:
Visualization and Interpretation of High Content Screening Data. 201-207 - Nikolaus Stiefl, Ian A. Watson, Knut Baumann
, Andrea Zaliani
:
ErG: 2D Pharmacophore Descriptions for Scaffold Hopping. 208-220
- Shinji Amari, Masahiro Aizawa, Junwei Zhang, Kaori Fukuzawa
, Yuji Mochizuki, Yoshio Iwasawa, Kotoko Nakata, Hiroshi Chuman, Tatsuya Nakano:
VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening. 221-230 - Matthew Clark
, Frank Guarnieri, Igor Shkurko, Jeffrey S. Wiseman:
Grand Canonical Monte Carlo Simulation of Ligand-Protein Binding. 231-242 - Niu Huang
, Chakrapani Kalyanaraman, John J. Irwin
, Matthew P. Jacobson
:
Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening. 243-253 - Philippe Ferrara, Alessandro Curioni, Eric Vangrevelinghe, T. Meyer, Tiziana Mordasini, Wanda Andreoni, Pierre Acklin, Edgar Jacoby:
New Scoring Functions for Virtual Screening from Molecular Dynamics Simulations with a Quantum-Refined Force-Field (QRFF-MD). Application to Cyclin-Dependent Kinase 2. 254-263 - Orazio Nicolotti
, Angelo Carotti:
QSAR and QSPR Studies of a Highly Structured Physicochemical Domain. 264-276 - J. Christian Baber, William A. Shirley, Yinghong Gao, Miklos Feher:
The Use of Consensus Scoring in Ligand-Based Virtual Screening. 277-288 - Prabha Garg
, Jitender Verma:
In Silico Prediction of Blood Brain Barrier Permeability: An Artificial Neural Network Model. 289-297 - Sung Jin Cho, Yaxiong Sun:
FLAME: A Program to Flexibly Align Molecules. 298-306 - Douglas J. Klein, Alexandru T. Balaban:
The Eight Classes of Positive-Curvature Graphitic Nanocones. 307-320 - Debojyoti Dutta, Rajarshi Guha, Peter C. Jurs, Ting Chen:
Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing. 321-333
- Debra L. Bautista, Deanna H. Morris, Lauren Stein, Wesley Asher
, Timothy Hammitt:
A Two Model Receptor System of the Alpha1D Adrenergic Receptor To Describe Interactions with Epinephrine and BMY7378. 334-344 - Osvaldo Andrade Santos-Filho
, Anton J. Hopfinger:
Structure-Based QSAR Analysis of a Set of 4-Hydroxy-5, 6-dihydropyrones as Inhibitors of HIV-1 Protease: An Application of the Receptor-Dependent (RD) 4D-QSAR Formalism. 345-354
- Shane D. Peterson, Wesley Schaal
, Anders Karlén:
Improved CoMFA Modeling by Optimization of Settings. 355-364 - Visvaldas Kairys
, Miguel X. Fernandes
, Michael K. Gilson:
Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study. 365-379 - Akifumi Oda, Keiichi Tsuchida, Tadakazu Takakura, Noriyuki Yamaotsu
, Shuichi Hirono:
Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein-Ligand Complexes. 380-391 - Minghu Song, Matthew Clark
:
Development and Evaluation of an in Silico Model for hERG Binding. 392-400 - Hongming Chen, Paul D. Lyne, Fabrizio Giordanetto, Timothy Lovell, Jin Li:
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. 401-415 - Tomasz Arodz, David A. Yuen, Arkadiusz Z. Dudek:
Ensemble of Linear Models for Predicting Drug Properties. 416-423 - Dirk Neumann
, Oliver Kohlbacher
, Christian Merkwirth, Thomas Lengauer:
A Fully Computational Model for Predicting Percutaneous Drug Absorption. 424-429
- Anders Wallqvist
, Ruili Huang, Narmada Thanki, David G. Covell:
Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition. 430-437 - Vicky Choi:
On Updating Torsion Angles of Molecular Conformations. 438-444
- Lianyi Han
, Honghuang Lin
, Ze-Rong Li, C. J. Zheng, Zhi Wei Cao, B. Xie, Yu Zong Chen
:
PEARLS: Program for Energetic Analysis of Receptor-Ligand System. 445-450
Volume 46, Number 2, March 2006
- Robert W. Snyder, Markus Wagener:
Seventh International Conference on Chemical Structures June 5-9, 2005 Noordwijkerhout, The Netherlands. 451
- Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender:
Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme. 452-461 - Jérôme Hert
, Peter Willett, David J. Wilton, Pierre Acklin, Kamal Azzaoui, Edgar Jacoby, Ansgar Schuffenhauer:
New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching. 462-470 - David J. Wilton, Robert F. Harrison
, Peter Willett, John S. Delaney
, Kevin Lawson, Graham Mullier:
Virtual Screening Using Binary Kernel Discrimination: Analysis of Pesticide Data. 471-477 - Beining Chen, Robert F. Harrison
, Kitsuchart Pasupa
, Peter Willett, David J. Wilton, David J. Wood, Xiao Qing Lewell:
Virtual Screening Using Binary Kernel Discrimination: Effect of Noisy Training Data and the Optimization of Performance. 478-486 - Egon L. Willighagen
, H. M. G. W. Denissen, Ron Wehrens
, Lutgarde M. C. Buydens:
On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors. 487-494 - David J. Wild, Gary Wiggins:
Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University. 495-502 - Edward J. Barker, David Buttar
, David A. Cosgrove, Eleanor J. Gardiner, Paula Kitts, Peter Willett, Valerie J. Gillet
:
Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. 503-511 - Mireille Krier
, Guillaume Bret, Didier Rognan:
Assessing the Scaffold Diversity of Screening Libraries. 512-524 - Ansgar Schuffenhauer, Nathan Brown, Paul Selzer, Peter Ertl
, Edgar Jacoby:
Relationships between Molecular Complexity, Biological Activity, and Structural Diversity. 525-535 - Modest von Korff, Thomas Sander:
Toxicity-Indicating Structural Patterns. 536-544 - Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck
, Adriaan P. IJzerman
:
The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. 545-552 - Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck
, Adriaan P. IJzerman
:
Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés". 553-562 - György Pirok, Nóra Máté, Jeno Varga, József Szegezdi, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia:
Making "Real" Molecules in Virtual Space. 563-568 - Sarah Rodgers, Robert C. Glen, Andreas Bender:
Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model. 569-576 - Kristian Birchall, Valerie J. Gillet
, Gavin Harper, Stephen D. Pickett:
Training Similarity Measures for Specific Activities: Application to Reduced Graphs. 577-586 - Nikolaus Stiefl, Andrea Zaliani
:
A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening. 587-596 - Jeroen Kazius, Siegfried Nijssen
, Joost N. Kok, Thomas Bäck
, Adriaan P. IJzerman
:
Substructure Mining Using Elaborate Chemical Representation. 597-605 - Ingrid M. Socorro, Jonathan M. Goodman
:
The ROBIA Program for Predicting Organic Reactivity. 606-614 - Nicholas Rhodes, David E. Clark, Peter Willett:
Similarity Searching in Databases of Flexible 3D Structures Using Autocorrelation Vectors Derived from Smoothed Bounded Distance Matrices. 615-619 - Pekka T. Lehtovuori, Tommi H. Nyrönen
:
SOMA - Workflow for Small Molecule Property Calculations on a Multiplatform Computing Grid. 620-625 - Dumitru Erhan
, Pierre-Jean L'Heureux, Shi Yi Yue, Yoshua Bengio:
Collaborative Filtering on a Family of Biological Targets. 626-635 - Ralph Kühne
, Ralf-Uwe Ebert, Gerrit Schüürmann
:
Model Selection Based on Structural Similarity-Method Description and Application to Water Solubility Prediction. 636-641 - Stuart Firth-Clark, Henriëtte M. G. Willems, Anthony Williams, William Harris:
Generation and Selection of Novel Estrogen Receptor Ligands Using the De Novo Structure-Based Design Tool, SkelGen. 642-647 - Andreas H. Göller, Matthias Hennemann
, Jörg Keldenich, Timothy Clark
:
In Silico Prediction of Buffer Solubility Based on Quantum-Mechanical and HQSAR- and Topology-Based Descriptors. 648-658 - Anna Maria Capelli, Aldo Feriani, Giovanna Tedesco, Alfonso Pozzan:
Generation of a Focused Set of GSK Compounds Biased toward Ligand-Gated Ion-Channel Ligands. 659-664 - Timothy J. Cheeseright, Mark D. Mackey, Sally Rose, Andy Vinter:
Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation. 665-676 - Markus Wagener, Jos P. M. Lommerse:
The Quest for Bioisosteric Replacements. 677-685 - Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Peter Willett:
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions. 686-698 - Uli Fechner, Gisbert Schneider
:
Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design. 699-707 - Monika Rella, Christopher A. Rushworth, Jodie L. Guy, Anthony J. Turner, Thierry Langer
, Richard M. Jackson:
Structure-Based Pharmacophore Design and Virtual Screening for Novel Angiotensin Converting Enzyme 2 Inhibitors. 708-716 - Esther Kellenberger, Pascal Muller, Claire Schalon, Guillaume Bret, Nicolas Foata, Didier Rognan:
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank. 717-727 - Samuel Toba, Jayashree Srinivasan, Allister J. Maynard, Jon M. Sutter:
Using Pharmacophore Models To Gain Insight into Structural Binding and Virtual Screening: An Application Study with CDK2 and Human DHFR. 728-735 - Nicola D. Gold, Richard M. Jackson:
A Searchable Database for Comparing Protein-Ligand Binding Sites for the Analysis of Structure-Function Relationships. 736-742 - Linda Hirons, Eleanor J. Gardiner, Christopher A. Hunter, Peter Willett:
Structural DNA Profiles: Single Sequence Queries. 743-752 - Eleanor J. Gardiner, Linda Hirons, Christopher A. Hunter, Peter Willett:
Genomic Data Analysis Using DNA Structure: An Analysis of Conserved Nongenic Sequences and Ultraconserved Elements. 753-761 - Joseph L. Durant, Burton A. Leland, James G. Nourse:
VET: A Tool for Reaction Plausibility Checking. 762-766
- A. Ben Wagner
:
SciFinder Scholar 2006: An Empirical Analysis of Research Topic Query Processing. 767-774 - Hideyuki Masui, Huixiao Hong
:
Spec2D: A Structure Elucidation System Based on 1H NMR and H-H COSY Spectra in Organic Chemistry. 775-787 - Jerry Ray Dias:
What Do We Know about C28H14 and C30H14 Benzenoid Hydrocarbons and Their Evolution to Related Polymer Strips?. 788-800 - Jenna L. Wang, Paul G. Mezey:
The Electronic Structures and Properties of Open-Ended and Capped Carbon Nanoneedles. 801-807 - Igor V. Tetko
, Vitaly P. Solov'ev
, Alexey V. Antonov, Xiaojun Yao, Jean-Pierre Doucet, Bo Tao Fan, Frank Hoonakker, Denis Fourches
, Piere Jost, Nicolas Lachiche
, Alexandre Varnek:
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores. 808-819 - W. Bradford Davis, Ray Hefferlin:
An Atlas of Forecasted Molecular Data. 2. Vibration Frequencies of Main-Group and Transition-Metal Neutral Gas-Phase Diatomic Molecules in the Ground State. 820-825 - W. Michael Brown, Shawn Martin, Mark D. Rintoul, Jean-Loup Faulon
:
Designing Novel Polymers with Targeted Properties Using the Signature Molecular Descriptor. 826-835 - David Vidal
, Michael Thormann, Miquel Pons
:
A Novel Search Engine for Virtual Screening of Very Large Databases. 836-843
- Scott Oloff, Shuxing Zhang, Nagamani Sukumar
, Curt M. Breneman, Alexander Tropsha:
Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). 844-851 - Giovanni Bottegoni
, Andrea Cavalli
, Maurizio Recanatini
:
A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. 852-862 - Wen Wu, Michael Daszykowski
, Beata Walczak
, Brian C. Sweatman, Susan C. Connor, John N. Haselden, Daniel J. Crowther, Rob W. Gill, Michael W. Lutz
:
Peak Alignment of Urine NMR Spectra Using Fuzzy Warping. 863-875 - John R. Goodell, Bengt Svensson, David M. Ferguson
:
Spectrophotometric Determination and Computational Evaluation of the Rates of Hydrolysis of 9-Amino-Substituted Acridines. 876-883 - Dimitri Gilis
, Christophe Biot
, Eric Buisine, Yves Dehouck
, Marianne Rooman:
Development of Novel Statistical Potentials Describing Cation-pi Interactions in Proteins and Comparison with Semiempirical and Quantum Chemistry Approaches. 884-893 - Rainer Brüggemann, Guillermo Restrepo
, Kristina Voigt:
Structure-Fate Relationships of Organic Chemicals Derived from the Software Packages E4CHEM and WHASSE. 894-902 - Andreas Kämper
, Joannis Apostolakis, Matthias Rarey
, Christel M. Marian
, Thomas Lengauer:
Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. 903-911 - Natalie Fey
, Stephanie E. Harris, Jeremy N. Harvey
, A. Guy Orpen:
Adding Value to Crystallographically-Derived Knowledge Bases. 912-929
- Hassan Modarresi, John C. Dearden, Hamid Modarress:
QSPR Correlation of Melting Point for Drug Compounds Based on Different Sources of Molecular Descriptors. 930-936
Volume 46, Number 3, May 2006
- William L. Jorgensen:
QSAR/QSPR and Proprietary Data. 937 - Sangtae Kim:
Cyberinfrastructure: Enabling the Chemical Sciences. 938
- Kieron R. Taylor
, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey
, Stephen W. Harris, David De Roure
:
Bringing Chemical Data onto the Semantic Web. 939-952 - Sulev Sild, Uko Maran
, Andre Lomaka, Mati Karelson:
Open Computing Grid for Molecular Science and Engineering. 953-959 - Robert J. Gledhill, Sarah Kent, Brian Hudson, W. Graham Richards, Jonathan W. Essex, Jeremy G. Frey
:
A Computer-Aided Drug Discovery System for Chemistry Teaching. 960-970 - Thanh N. Truong, Manohar Nayak, Hung H. Huynh, Tom Cook, Priya Mahajan, Le-Thuy T. Tran, Jannu Bharath, Shrish Jain, Ha B. Pham, Chaiwoot Boonyasiriwat, Nhat Nguyen, Evan Andersen, Yong Kim, Suengkeol Choe, Jihoon Choi, Thomas E. Cheatham III, Julio C. Facelli
:
Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. 971-984 - Henry S. Rzepa, Andrew Wheat, Mark J. Williamson:
ChemSem: An Extensible and Scalable RSS-Based Seminar Alerting System for Scientific Collaboration. 985-990 - Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison
, Peter Murray-Rust, Henry S. Rzepa, Christoph Steinbeck
, Jörg K. Wegner
, Egon L. Willighagen
:
The Blue Obelisk-Interoperability in Chemical Informatics. 991-998 - Scott P. Brown, Steven W. Muchmore:
High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing. 999-1005 - Simon J. Coles
, Jeremy G. Frey
, Michael B. Hursthouse, Mark E. Light
, Andrew J. Milsted
, Leslie Carr
, David De Roure
, Christopher Gutteridge, Hugo R. Mills, Ken Meacham, Mike Surridge, Elizabeth Josephine Lyon, Rachel Heery, Monica Duke
, Michael Day
:
An E-Science Environment for Service Crystallography-from Submission to Dissemination. 1006-1016 - Randall Bramley, Kenneth Chiu, Tharaka Devadithya, Nisha Gupta, Charles A. Hart, John C. Huffman, Kianosh Huffman, Yu Ma, Donald F. McMullen:
Instrument Monitoring, Data Sharing, and Archiving Using Common Instrument Middleware Architecture (CIMA). 1017-1025 - Matt J. Harvey
, Daniel J. Scott, Peter V. Coveney:
An Integrated Instrument Control and Informatics System for Combinatorial Materials Research. 1026-1033 - Peter Lind, Markus Alm:
A Database-Centric Virtual Chemistry System. 1034-1039
- Michael Thormann, Andreas Klamt
, Martin Hornig, Michael Almstetter:
COSMOsim: Bioisosteric Similarity Based on COSMO-RS sigma Profiles. 1040-1053 - Fumiyoshi Yamashita
, Takayuki Itoh, Hideto Hara, Mitsuru Hashida
:
Visualization of Large-Scale Aqueous Solubility Data Using a Novel Hierarchical Data Visualization Technique. 1054-1059 - Bradley C. Pearce, Michael J. Sofia, Andrew C. Good, Dieter M. Drexler
, David A. Stock:
An Empirical Process for the Design of High-Throughput Screening Deck Filters. 1060-1068 - Ramaswamy Nilakantan, David S. Nunn, Lynne Greenblatt, Gary Walker, Kevin S. Haraki, Dominick Mobilio:
A Family of Ring System-Based Structural Fragments for Use in Structure-Activity Studies: Database Mining and Recursive Partitioning. 1069-1077 - Alireza Givehchi, Andreas Bender, Robert C. Glen:
Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors. 1078-1083 - Surjit B. Dixit, Sergei Y. Ponomarev, David L. Beveridge:
Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA. 1084-1093 - Jeffrey W. Godden, Jürgen Bajorath:
A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations. 1094-1097 - Dariusz Plewczynski
, Stéphane A. H. Spieser, Uwe Koch:
Assessing Different Classification Methods for Virtual Screening. 1098-1106 - Alex M. Clark
, Paul Labute, Martin Santavy:
2D Structure Depiction. 1107-1123 - Nidhi, Meir Glick, John W. Davies, Jeremy L. Jenkins
:
Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases. 1124-1133
- Nikolay P. Todorov, Philippe H. Monthoux, Ian L. Alberts:
The Influence of Variations of Ligand Protonation and Tautomerism on Protein-Ligand Recognition and Binding Energy Landscape. 1134-1142 - Mohammad Wasim
, Richard G. Brereton:
Hard Modeling Methods for the Curve Resolution of Data from Liquid Chromatography with a Diode Array Detector and On-Flow Liquid Chromatography with Nuclear Magnetic Resonance Spectroscopy. 1143-1153 - Anton Lindström, Fredrik Pettersson, Fredrik Almqvist
, Anders Berglund
, Jan Kihlberg, Anna Linusson:
Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein-Ligand Complexes. 1154-1167 - Stuart Firth-Clark, Nikolay P. Todorov, Ian L. Alberts, Anthony Williams, Timothy James, Philip M. Dean:
Exhaustive de novo Design of Low-Molecular-Weight Fragments Against the ATP-Binding Site of DNA-Gyrase. 1168-1173 - Laleh Alisaraie, Lars A. Haller, Gregor Fels:
A QXP-Based Multistep Docking Procedure for Accurate Prediction of Protein-Ligand Complexes. 1174-1187 - Philippa R. N. Wolohan, Lakshmi B. Akella, Roman J. Dorfman, Peter G. Nell, Stefan M. Mundt, Robert D. Clark:
Structural Unit Analysis Identifies Lead Series and Facilitates Scaffold Hopping in Combinatorial Chemistry. 1188-1193 - Milan Remko, Claus-Wilhelm von der Lieth:
Gas-Phase and Solution Conformations of the alpha-L-Iduronic Acid Structural Unit of Heparin. 1194-1200 - Thierry Kogej, Ola Engkvist
, Niklas Blomberg
, Sorel Muresan
:
Multifingerprint Based Similarity Searches for Targeted Class Compound Selection. 1201-1213 - Artem Cherkasov:
Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?. 1214-1222 - Alessandra Fano, David W. Ritchie
, Antonio Carrieri
:
Modeling the Structural Basis of Human CCR5 Chemokine Receptor Function: From Homology Model Building and Molecular Dynamics Validation to Agonist and Antagonist Docking. 1223-1235 - Deepangi Pandit, Sung-Sau So, Hongmao Sun:
Enhancing Specificity and Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Chemical and Shape Features-A Case Study of HIV Protease Inhibitors. 1236-1244 - Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha:
Combinatorial QSAR Modeling of P-Glycoprotein Substrates. 1245-1254 - Julio Caballero
, Leyden Fernández, José Ignacio Abreu
, Michael Fernández
:
Amino Acid Sequence Autocorrelation Vectors and Ensembles of Bayesian-Regularized Genetic Neural Networks for Prediction of Conformational Stability of Human Lysozyme Mutants. 1255-1268 - Mamoru Sakai, Kazuo Toyota, Takeji Takui:
A Quantum and Deductive Chemical Study for All Congeners of Polybromo/Chlorodibenzo-p-dioxin and Polybromo/Chlorodibenzofuran. 1269-1275
- Toshiaki Matsubara, Masashi Ishikura, Misako Aida
:
A Quantum Chemical Study of the Catalysis for Cytidine Deaminase: Contribution of the Extra Water Molecule. 1276-1285 - Joong-Youn Shim, Allyn C. Howlett
:
WIN55212-2 Docking to the CB1 Cannabinoid Receptor and Multiple Pathways for Conformational Induction. 1286-1300
- Daniela Schuster
, Christian Laggner, Theodora M. Steindl, Anja Palusczak, Rolf W. Hartmann, Thierry Langer
:
Pharmacophore Modeling and in Silico Screening for New P450 19 (Aromatase) Inhibitors. 1301-1311 - Munikumar Reddy Doddareddy, Yong Seo Cho, Hun Yeong Koh, Dong Hyun Kim
, Ae Nim Pae:
In Silico Renal Clearance Model Using Classical Volsurf Approach. 1312-1320 - Tulay Ercanli, Donald B. Boyd:
Exploration of the Conformational Space of a Polymeric Material that Inhibits Human Immunodeficiency Virus. 1321-1333 - Micael Jacobsson, Anders Karlén:
Ligand Bias of Scoring Functions in Structure-Based Virtual Screening. 1334-1343 - Fabrizio Manetti
, Cristina Tintori, Mercedes Armand-Ugón
, Imma Clotet-Codina, Silvio Massa, Rino Ragno
, José A. Esté, Maurizio Botta:
A Combination of Molecular Dynamics and Docking Calculations to Explore the Binding Mode of ADS-J1, a Polyanionic Compound Endowed with Anti-HIV-1 Activity. 1344-1351 - Jun Feng, Ashish P. Sanil, S. Stanley Young:
PharmID: Pharmacophore Identification Using Gibbs Sampling. 1352-1359 - Nidhi Singh, Gwénaël Chevé
, Mitchell A. Avery, Christopher R. McCurdy:
Comparative Protein Modeling of 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Enzyme from Plasmodium falciparum: A Potential Target for Antimalarial Drug Discovery. 1360-1370 - Katsumi Yoshida, Tomoko Niwa:
Quantitative Structure-Activity Relationship Studies on Inhibition of HERG Potassium Channels. 1371-1378 - Pierre Bruneau, Nathan R. McElroy:
logD7.4 Modeling Using Bayesian Regularized Neural Networks. Assessment and Correction of the Errors of Prediction. 1379-1387 - Xavier Gironés, Robert Ponec:
Molecular Quantum Similarity Measures from Fermi Hole Densities: Modeling Hammett Sigma Constants. 1388-1393 - Dhrubajyoti Biswas, Sujata Roy
, Srikanta Sen:
A Simple Approach for Indexing the Oral Druglikeness of a Compound: Discriminating Druglike Compounds from Nondruglike Ones. 1394-1401 - Sven Serneels
, Evert De Nolf, Pierre J. Van Espen:
Spatial Sign Preprocessing: A Simple Way To Impart Moderate Robustness to Multivariate Estimators. 1402-1409 - Eric Deconinck, Menghui H. Zhang, Danny Coomans, Yvan Vander Heyden:
Classification Tree Models for the Prediction of Blood-Brain Barrier Passage of Drugs. 1410-1419 - Rino Ragno
, Silvia Simeoni, Sergio Valente
, Silvio Massa, Antonello Mai
:
3-D QSAR Studies on Histone Deacetylase Inhibitors. A GOLPE/GRID Approach on Different Series of Compounds. 1420-1430 - Máté Dervarics, Ferenc Ötvös, Tamás A. Martinek:
Development of a Chirality-Sensitive Flexibility Descriptor for 3+3D-QSAR. 1431-1438 - Joan R. Cucarull-González, Christian Laggner, Thierry Langer
:
Influence of the Conditions in Pharmacophore Generation, Scoring, and 3D Database Search for Chemical Feature-Based Pharmacophore Models: One Application Study of ETA- and ETB-Selective Antagonists. 1439-1455 - Markus H. J. Seifert:
Assessing the Discriminatory Power of Scoring Functions for Virtual Screening. 1456-1465 - Laura Maccari, Matteo Magnani, Giovannella Strappaghetti, Federico Corelli, Maurizio Botta, Fabrizio Manetti
:
A Genetic-Function-Approximation-Based QSAR Model for the Affinity of Arylpiperazines toward alpha1 Adrenoceptors. 1466-1478
- Joji M. Otaki, Akihito Mori, Yoshimasa Itoh, Takashi Nakayama, Haruhiko Yamamoto:
Alignment-Free Classification of G-Protein-Coupled Receptors Using Self-Organizing Maps. 1479-1490 - Channa K. Hattotuwagama, Christopher P. Toseland
, Pingping Guan, Debra J. Taylor, Shelley L. Hemsley, Irini A. Doytchinova
, Darren R. Flower:
Toward Prediction of Class II Mouse Major Histocompatibility Complex Peptide Binding Affinity: in Silico Bioinformatic Evaluation Using Partial Least Squares, a Robust Multivariate Statistical Technique. 1491-1502 - M. Michael Gromiha, Samuel Selvaraj, A. Mary Thangakani:
A Statistical Method for Predicting Protein Unfolding Rates from Amino Acid Sequence. 1503-1508 - Dimitri Gilis
:
In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic alpha-Amylases upon Exhaustive Single-Site Mutations. 1509-1516
- Cindy Benod, Marc-André Delsuc
, Jean-Luc Pons:
CRAACK: Consensus Program for NMR Amino Acid Type Assignment. 1517-1522 - Salvador Sagrado
, Mark T. D. Cronin:
Diagnostic Tools to Determine the Quality of "Transparent" Regression-Based QSARs: The "Modelling Power" Plot. 1523-1532
Volume 46, Number 4, July 2006
- Gerald M. Maggiora
:
On Outliers and Activity Cliffs-Why QSAR Often Disappoints. 1535
- Jean-François Truchon, Christopher I. Bayly:
GLARE: A New Approach for Filtering Large Reagent Lists in Combinatorial Library Design Using Product Properties. 1536-1548 - Justin Klekota, Erik Brauner, Frederick P. Roth
, Stuart L. Schreiber:
Using High-Throughput Screening Data To Discriminate Compounds with Single-Target Effects from Those with Side Effects. 1549-1562 - Alexandru T. Balaban, Thomas G. Schmalz:
Strain-Free Sextet-Resonant Benzenoids and Their Antisextet Dualists. 1563-1579 - Modest von Korff, Kurt Hilpert:
Assessing the Predictive Power of Unsupervised Visualization Techniques to Improve the Identification of GPCR-Focused Compound Libraries. 1580-1587 - Sara H. Fitzgerald, Michal Sabat, H. Mario Geysen:
Diversity Space and Its Application to Library Selection and Design. 1588-1597 - Aleksandr Y. Sedykh, Gilles Klopman:
A Structural Analogue Approach to the Prediction of the Octanol-Water Partition Coefficient. 1598-1603 - Thy-Hou Lin, Shih-Hau Chiu, Keng-Chang Tsai
:
Supervised Feature Ranking Using a Genetic Algorithm Optimized Artificial Neural Network. 1604-1614 - Elisabet Gregori-Puigjané, Jordi Mestres
:
SHED: Shannon Entropy Descriptors from Topological Feature Distributions. 1615-1622 - Hanna Eckert
, Ingo Vogt, Jürgen Bajorath:
Mapping Algorithms for Molecular Similarity Analysis and Ligand-Based Virtual Screening: Design of DynaMAD and Comparison with MAD and DMC. 1623-1634
- Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher
:
SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions. 1635-1642 - Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams
, Sergey G. Molodtsov, Gary E. Martin:
Are Deterministic Expert Systems for Computer-Assisted Structure Elucidation Obsolete?. 1643-1656 - Joaquim Chaves Martinez, Joan M. Barroso, Patrick Bultinck
, Ramon Carbó-Dorca
:
Toward an Alternative Hardness Kernel Matrix Structure in the Electronegativity Equalization Method (EEM). 1657-1665 - Elena Soriano, José Marco-Contelles, Cyrille Tomassi, Albert Nguyen Van Nhien, Denis Postel:
Computational Analysis of Aza Analogues of [2', 5'-Bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5' '- (4' '-amino-1' ', 2' '-oxathiole-2' ', 2' '-dioxide) (TSAO) as HIV-1 Reverse Transcriptase Inhibitors: Relevance of Conformational Properties on the Inhibitory Activity. 1666-1677 - Manuel Urbano-Cuadrado, Irene Luque Ruiz
, Miguel Ángel Gómez-Nieto
:
A Steroids QSAR Approach Based on Approximate Similarity Measurements. 1678-1686 - Milan Remko, Claus-Wilhelm von der Lieth:
Gas-Phase and Solution Conformations of Selected Dimeric Structural Units of Heparin. 1687-1694 - Andreas Steffen, Andreas Kämper
, Thomas Lengauer:
Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm. 1695-1703 - Stéphane Betzi, Karsten Suhre
, Bernard Chétrit, Françoise Guerlesquin, Xavier Morelli
:
GFscore: A General Nonlinear Consensus Scoring Function for High-Throughput Docking. 1704-1712 - Rajarshi Guha, Debojyoti Dutta, Peter C. Jurs, Ting Chen:
R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method. 1713-1722 - Paul Laffort, Pierre Héricourt:
Solvation Parameters. 2. A Simplified Molecular Topology to Generate Easily Optimized Values. 1723-1734 - Michael H. Abraham, Adam Ibrahim:
Gas to Olive Oil Partition Coefficients: A Linear Free Energy Analysis. 1735-1741
- Yan Li:
Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core. 1742-1750 - Noel Ferro
, Ana Gallegos
, Patrick Bultinck
, Hans-Jörg Jacobsen, Ramon Carbó-Dorca
, Thomas Reinard
:
Coulomb and Overlap Self-Similarities: A Comparative Selectivity Analysis of Structure-Function Relationships for Auxin-like Molecules. 1751-1762 - Pooja Sharma, Nanda Ghoshal:
Exploration of a Binding Mode of Benzothiazol-2-yl Acetonitrile Pyrimidine Core Based Derivatives as Potent c-Jun N-Terminal Kinase-3 Inhibitors and 3D-QSAR Analyses. 1763-1774 - Elizabeth A. Amin, William J. Welsh:
Highly Predictive CoMFA and CoMSIA Models for Two Series of Stromelysin-1 (MMP-3) Inhibitors Elucidate S1' and S1-S2' Binding Modes. 1775-1783
- K. V. V. M. Sai Ram, G. Rambabu, J. A. R. P. Sarma, Gautam R. Desiraju:
Ligand Coordinate Analysis of SC-558 from the Active Site to the Surface of COX-2: A Molecular Dynamics Study. 1784-1794 - Tímea Polgár
, György M. Keserü
:
Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase. 1795-1805 - Dharmesh M. Maniyar, Ian T. Nabney
, Bruce S. Williams, Andreas Sewing:
Data Visualization during the Early Stages of Drug Discovery. 1806-1818 - Xiao-Lei Zhu, Li Zhang, Qiong Chen, Jian Wan, Guangfu Yang:
Interactions of Aryloxyphenoxypropionic Acids with Sensitive and Resistant Acetyl-Coenzyme A Carboxylase by Homology Modeling and Molecular Dynamic Simulations. 1819-1826 - Hong Liang, Xing Wu, Lynn J. Guziec, Frank S. Guziec Jr., Kimberly K. Larson, Jennifer Lang, Jack C. Yalowich
, Brian B. Hasinoff:
A Structure-Based 3D-QSAR Study of Anthrapyrazole Analogues of the Anticancer Agents Losoxantrone and Piroxantrone. 1827-1835 - Rajarshi Guha, Debojyoti Dutta, Peter C. Jurs, Ting Chen:
Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions. 1836-1847 - Johannes Kirchmair
, Gerhard Wolber
, Christian Laggner, Thierry Langer
:
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. 1848-1861
- Alex Strizhev, Edmond J. Abrahamian, Sun Choi
, Joseph M. Leonard, Philippa R. N. Wolohan, Robert D. Clark
:
The Effects of Biasing Torsional Mutations in a Conformational GA. 1862-1870
- Brian Palmer, Joseph F. Danzer, Kevin Hambly, Derek A. Debe:
StructSorter: A Method for Continuously Updating a Comprehensive Protein Structure Alignment Database. 1871-1876
Volume 46, Number 5, September 2006
- Christina Mintz, William E. Acree Jr., Michael H. Abraham:
Comments on "Solvation Parameters, 2. A Simplified Molecular Topology To Generate Easily Optimized Values". 1879-1881
- Martin Bohl, Björn Loeprecht, Bernd Wendt, Trevor W. Heritage, Nicola J. Richmond, Peter Willett:
Unsupervised 3D Ring Template Searching as an Ideas Generator for Scaffold Hopping: Use of the LAMDA, RigFit, and Field-Based Similarity Search (FBSS) Methods. 1882-1890 - Mati Karelson, Dimitar A. Dobchev
, Oleksandr V. Kulshyn, Alan R. Katritzky:
Neural Networks Convergence Using Physicochemical Data. 1891-1897 - Ákos Papp, Anna Gulyás-Forró, Zsolt Gulyás, György Dormán
, László Ürge, Ferenc Darvas
:
Explicit Diversity Index (EDI): A Novel Measure for Assessing the Diversity of Compound Databases. 1898-1904 - Roberto Todeschini
, Viviana Consonni
, Andrea Mauri, Davide Ballabio
:
Characterization of DNA Primary Sequences by a New Similarity/Diversity Measure Based on the Partial Ordering. 1905-1911 - J. Andrew Grant, James A. Haigh, Barry T. Pickup
, Anthony Nicholls, Roger A. Sayle
:
Lingos, Finite State Machines, and Fast Similarity Searching. 1912-1918 - Weizhong Li
:
A Fast Clustering Algorithm for Analyzing Highly Similar Compounds of Very Large Libraries. 1919-1923 - Peter Gedeck
, Bernhard Rohde, Christian Bartels
:
QSAR - How Good Is It in Practice? Comparison of Descriptor Sets on an Unbiased Cross Section of Corporate Data Sets. 1924-1936 - José Batista
, Jeffrey W. Godden, Jürgen Bajorath:
Assessment of Molecular Similarity from the Analysis of Randomly Generated Structural Fragment Populations. 1937-1944 - Anthony E. Klon, Jeffrey F. Lowrie, David J. Diller
:
Improved Naïve Bayesian Modeling of Numerical Data for Absorption, Distribution, Metabolism and Excretion (ADME) Property Prediction. 1945-1956
- Zoran Markovic
, Svetlana Markovic
, Nebojsa Begovic:
Influence of Alkali Metal Cations upon the Kolbe-Schmitt Reaction Mechanism. 1957-1964 - Jenna L. Wang, Gerald H. Lushington
, Paul G. Mezey:
Stability and Electronic Properties of Nitrogen Nanoneedles and Nanotubes. 1965-1971 - Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen
, Chris Oostenbrink
:
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method. 1972-1983 - Shuxing Zhang, Alexander Golbraikh, Scott Oloff, Harold Kohn, Alexander Tropsha:
A Novel Automated Lazy Learning QSAR (ALL-QSAR) Approach: Method Development, Applications, and Virtual Screening of Chemical Databases Using Validated ALL-QSAR Models. 1984-1995 - Qi Chen
, Richard E. Higgs, Michal Vieth:
Geometric Accuracy of Three-Dimensional Molecular Overlays. 1996-2002 - Pierre Mahé, Liva Ralaivola, Véronique Stoven, Jean-Philippe Vert
:
The Pharmacophore Kernel for Virtual Screening with Support Vector Machines. 2003-2014 - Mafalda M. Dias, Ruchi R. Mittal, Ross A. McKinnon
, Michael J. Sorich
:
Systematic Statistical Comparison of Comparative Molecular Similarity Indices Analysis Molecular Fields for Computer-Aided Lead Optimization. 2015-2021 - Manuel Urbano-Cuadrado, Irene Luque Ruiz
, Miguel Ángel Gómez-Nieto
:
Refinement and Use of the Approximate Similarity in QSAR Models for Benzodiazepine Receptor Ligands. 2022-2029 - Luca Bernazzani
, Celia Duce
, Alessio Micheli
, Vincenzo Mollica, Alessandro Sperduti, Antonina Starita, Maria Rosaria Tiné
:
Predicting Physical-Chemical Properties of Compounds from Molecular Structures by Recursive Neural Networks. 2030-2042 - Subhash Ajmani, Stephen C. Rogers, Mark H. Barley, David J. Livingstone:
Application of QSPR to Mixtures. 2043-2055 - Luis Lorenzo, María J. González-Moa, Marcos Mandado
, Ricardo A. Mosquera
:
Do the Neighboring Residues in a Polypeptide Affect the Electron Distribution of an Amino Acid Significantly? A Quantitative Study Using the Quantum Theory of Atoms in Molecules (QTAIM). 2056-2065 - Hiroshi Takeuchi:
Clever and Efficient Method for Searching Optimal Geometries of Lennard-Jones Clusters. 2066-2070
- Yoshifumi Fukunishi
, Satoru Kubota, Haruki Nakamura:
Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. 2071-2084 - Ornjira Aruksakunwong, Peter Wolschann, Supot Hannongbua, Pornthep Sompornpisut:
Molecular Dynamic and Free Energy Studies of Primary Resistance Mutations in HIV-1 Protease-Ritonavir Complexes. 2085-2092 - Tatsusada Yoshida, Zsolt Lepp, Yoshito Kadota
, Yurie Satoh, Kohji Itoh, Hiroshi Chuman:
Comparative Analysis of Binding Energy of Chymostatin with Human Cathepsin A and Its Homologous Proteins by Molecular Orbital Calculation. 2093-2103 - Elizabeth A. Amin, William J. Welsh:
A Preliminary in Silico Lead Series of 2-Phthalimidinoglutaric Acid Analogues Designed as MMP-3 Inhibitors. 2104-2109
- Milan Ganguly, Nathan Brown, Ansgar Schuffenhauer, Peter Ertl
, Valerie J. Gillet, Paulette A. Greenidge:
Introducing the Consensus Modeling Concept in Genetic Algorithms: Application to Interpretable Discriminant Analysis. 2110-2124 - Boryeu Mao, Rafael Gozalbes
, Frédérique Barbosa, Jacques Migeon, Sandra Merrick, Kelly Kamm, Eric Wong, Chester Costales
, Wei Shi, Cheryl Wu, Nicolas Froloff:
QSAR Modeling of in Vitro Inhibition of Cytochrome P450 3A4. 2125-2134 - Markus A. Lill
, Angelo Vedani:
Combining 4D Pharmacophore Generation and Multidimensional QSAR: Modeling Ligand Binding to the Bradykinin B2 Receptor. 2135-2145 - Theodora M. Steindl, Daniela Schuster
, Christian Laggner, Thierry Langer
:
Parallel Screening: A Novel Concept in Pharmacophore Modeling and Virtual Screening. 2146-2157
- Tomoko Niwa:
Elucidation of Characteristic Structural Features of Ligand Binding Sites of Protein Kinases: A Neural Network Approach. 2158-2166 - Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov:
Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. 2167-2182 - Laavanya Parthasarathi, Marc Devocelle
, Chresten R. Søndergaard, Ivan Baran, Colm O'Dushlaine, Norman E. Davey
, Richard J. Edwards
, Niamh Moran, Dermot Kenny
, Denis C. Shields:
Absolute Net Charge and the Biological Activity of Oligopeptides. 2183-2190
Volume 46, Number 6, November 2006
These articles are in appreciation for Dr. Johann Gasteiger's contribution to chemoinformatics
- Thomas Engel:
Johann Gasteiger - Germany's Pioneer in Chemoinformatics. 2191-2192
- Martin Whittle, Valerie J. Gillet
, Peter Willett, Jens Loesel:
Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model. 2193-2205 - Martin Whittle, Valerie J. Gillet
, Peter Willett, Jens Loesel:
Analysis of Data Fusion Methods in Virtual Screening: Similarity and Group Fusion. 2206-2219 - Alexander Böcker, Gisbert Schneider
, Andreas Teckentrup:
NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening. 2220-2229 - William Lingran Chen:
Chemoinformatics: Past, Present, and Future†. 2230-2255 - Jinhua Zhang, Thomas Kleinöder, Johann Gasteiger:
Prediction of pKa Values for Aliphatic Carboxylic Acids and Alcohols with Empirical Atomic Charge Descriptors. 2256-2266 - Thomas Engel
:
Basic Overview of Chemoinformatics. 2267-2277 - Qing-You Zhang, João Aires-de-Sousa
:
Physicochemical Stereodescriptors of Atomic Chiral Centers. 2278-2287 - M. Leonor Contreras, José Alvarez, D. Guajardo, Roberto Rozas:
Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation. 2288-2298 - Aixia Yan
:
Modeling of Gibbs Energy of Formation of Organic Compounds by Linear and Nonlinear Methods. 2299-2304 - Jens Sadowski, Jonas Boström:
MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-ray Structures. 2305-2309 - Jaroslaw Polanski
, Andrzej Bak, Rafal Gieleciak, Tomasz Magdziarz:
Modeling Robust QSAR. 2310-2318 - Paul Selzer, Peter Ertl
:
Applications of Self-Organizing Neural Networks in Virtual Screening and Diversity Selection. 2319-2323 - Steffen Renner, Christof H. Schwab, Johann Gasteiger, Gisbert Schneider
:
Impact of Conformational Flexibility on Three-Dimensional Similarity Searching Using Correlation Vectors. 2324-2332 - Martin Reitz, Alexander von Homeyer, Johann Gasteiger:
Query Generation to Search for Inhibitors of Enzymatic Reactions. 2333-2341 - Frank Oellien
, Jörg Cramer, Carsten Beyer, Wolf-Dietrich Ihlenfeldt, Paul M. Selzer:
The Impact of Tautomer Forms on Pharmacophore-Based Virtual Screening. 2342-2354
- Punnaivanam Sankar, Gnanasekaran Aghila:
Design and Development of Chemical Ontologies for Reaction Representation. 2355-2368 - Edward O. Cannon, Andreas Bender, David S. Palmer
, John B. O. Mitchell
:
Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport. 2369-2380 - S. Frank Yan, Frederick J. King, Yun He, Jeremy S. Caldwell, Yingyao Zhou:
Learning from the Data: Mining of Large High-Throughput Screening Databases. 2381-2395 - Ömer Casher, Henry S. Rzepa:
SemanticEye: A Semantic Web Application to Rationalize and Enhance Chemical Electronic Publishing. 2396-2411 - Florian Nigsch
, Andreas Bender, Bernd van Buuren
, Jos Tissen, Eduard Nigsch
, John B. O. Mitchell
:
Melting Point Prediction Employing k-Nearest Neighbor Algorithms and Genetic Parameter Optimization. 2412-2422 - Todd Ewing, J. Christian Baber, Miklos Feher:
Novel 2D Fingerprints for Ligand-Based Virtual Screening. 2423-2431 - Andreas Karwath
, Luc De Raedt
:
SMIREP: Predicting Chemical Activity from SMILES. 2432-2444 - Andreas Bender, Jeremy L. Jenkins
, Meir Glick, Zhan Deng, James H. Nettles, John W. Davies:
"Bayes Affinity Fingerprints" Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept? 2445-2456 - Fanny Bonachéra, Benjamin Parent, Frédérique Barbosa, Nicolas Froloff, Dragos Horvath:
Fuzzy Tricentric Pharmacophore Fingerprints, 1. Topological Fuzzy Pharmacophore Triplets and Adapted Molecular Similarity Scoring Schemes. 2457-2477 - S. Bhavani, Aparna Nagargadde, Amit Thawani, V. Sridhar, N. Chandra:
Substructure-Based Support Vector Machine Classifiers for Prediction of Adverse Effects in Diverse Classes of Drugs. 2478-2486 - Michael Frenkel, Robert D. Chirico, Vladimir V. Diky, Chris Muzny, Qian Dong
, Kenneth N. Marsh, John H. Dymond, William A. Wakeham, Stephen E. Stein, Erich Königsberger
, Anthony R. H. Goodwin, Joseph W. Magee, Michiel Thijssen
, William M. Haynes, Suphat Watanasiri, Marco Satyro, Martin Schmidt, Andrew I. Johns, Gary R. Hardin:
New Global Communication Process in Thermodynamics: Impact on Quality of Published Experimental Data. 2487-2493 - Yan-Ping Zhou, Jian-Hui Jiang, Wei-Qi Lin, Hong-Yan Zou
, Hai-Long Wu, Guo-Li Shen, Ru-Qin Yu:
Adaptive Configuring of Radial Basis Function Network by Hybrid Particle Swarm Algorithm for QSAR Studies of Organic Compounds. 2494-2501 - Jens Auer, Jürgen Bajorath:
Emerging Chemical Patterns: A New Methodology for Molecular Classification and Compound Selection. 2502-2514 - Hanna Eckert
, Jürgen Bajorath:
Design and Evaluation of a Novel Class-Directed 2D Fingerprint to Search for Structurally Diverse Active Compounds. 2515-2526
- Robert Izsak
, Balázs Jójárt, Imre G. Csizmadia, Béla Viskolcz
:
Role of Aromacity, Ring Strain, and Stereochemistry of Selected Disulfides and Their Congeners in the Oxidative Linkage of DNA Strands at the Major Groove. A Computational Study. 2527-2536 - Nikolai Nikolov, Vanjo Grancharov, Galya Stoyanova, Todor Pavlov, Ovanes Mekenyan:
Representation of Chemical Information in OASIS Centralized 3D Database for Existing Chemicals. 2537-2551 - Hideyuki Sato, Lisa M. Shewchuk, Jun Tang:
Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance. 2552-2562 - Arthur M. Doweyko, Stephen R. Johnson:
A Novel Method to Simulate the Hydrophobic Effect and Its Application to the Ranking of Host/Guest Complexes. 2563-2573 - Aniela E. Vizitiu, Mircea V. Diudea
, Sonja Nikolic
, Dusanka Janezic:
Retro-Leapfrog and Related Retro Map Operations. 2574-2578 - Gyanendra Pandey, Anil K. Saxena:
3D QSAR Studies on Protein Tyrosine Phosphatase 1B Inhibitors: Comparison of the Quality and Predictivity among 3D QSAR Models Obtained from Different Conformer-Based Alignments. 2579-2590 - Ralph A. Mansson, Alan H. Welsh
, Natalie Fey
, A. Guy Orpen:
Statistical Modeling of a Ligand Knowledge Base. 2591-2600 - Niclas Tue Hansen, Irene Kouskoumvekaki
, Flemming Steen Jørgensen
, Søren Brunak
, Svava Ósk Jónsdóttir:
Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules. 2601-2609
- Yoshifumi Fukunishi
, Shinichi Hojo, Haruki Nakamura:
An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands. 2610-2622 - Tao Zhang, Xi-Cheng Dong, Min-Bo Chen:
Recognition of LXXLL by Ligand Binding Domain of the Farnesoid X Receptor in Molecular Dynamics Simulation. 2623-2630 - Ryan G. Coleman
, Anna C. Salzberg, Alan C. Cheng
:
Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model. 2631-2637
- Grégori Gerebtzoff, Anna Seelig:
In Silico Prediction of Blood-Brain Barrier Permeation Using the Calculated Molecular Cross-Sectional Area as Main Parameter. 2638-2650 - Michael F. M. Engels, Alan C. Gibbs
, Edward P. Jaeger, Danny Verbinnen, Victor S. Lobanov, Dimitris K. Agrafiotis
:
A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition. 2651-2660 - Matthew J. Sykes
, Michael J. Sorich
, John O. Miners
:
Molecular Modeling Approaches for the Prediction of the Nonspecific Binding of Drugs to Hepatic Microsomes. 2661-2673 - Junmei Wang
, George Krudy, Xiang-Qun Xie, Chengde Wu, George Holland:
Genetic Algorithm-Optimized QSPR Models for Bioavailability, Protein Binding, and Urinary Excretion. 2674-2683 - Jing Chen, Luhua Lai:
Pocket v.2: Further Developments on Receptor-Based Pharmacophore Modeling. 2684-2691 - Michael J. Sorich
, Ross A. McKinnon
, John O. Miners
, Paul A. Smith
:
The Importance of Local Chemical Structure for Chemical Metabolism by Human Uridine 5'-Diphosphate-Glucuronosyltransferase. 2692-2697 - Peter S. Bazeley, Sridevi Prithivi, Craig A. Struble, Richard J. Povinelli
, Daniel S. Sem
:
Synergistic Use of Compound Properties and Docking Scores in Neural Network Modeling of CYP2D6 Binding: Predicting Affinity and Conformational Sampling. 2698-2708 - Ernesto Estrada
, Eugenio Uriarte
, Enrique Molina Pérez, Yamil Simón-Manso
, George W. A. Milne:
An Integrated in Silico Analysis of Drug-Binding to Human Serum Albumin. 2709-2724 - Jordi Mestres
, Lidia Martín-Couce, Elisabet Gregori-Puigjané, Montserrat Cases, Scott Boyer:
Ligand-Based Approach to In Silico Pharmacology: Nuclear Receptor Profiling. 2725-2736 - Alexander Weber
, Markus Böhm, Claudiu T. Supuran
, Andrea Scozzafava
, Christoph A. Sotriffer, Gerhard Klebe:
3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors. 2737-2760
- Anselm H. C. Horn:
A Guide to Biomolecular Simulations By Oren M. Becker and Martin Karplus. Series: Focus on Structural Biology; Springer, Dordrecht, 2006. Vol 4, 220 pp. ISBN 1-4020-3586-1. Hardcover U.S. $89.95, Euro74.95. 2761
- Kai Ludwig, Bernd Speiser:
EChem++ An Object-Oriented Problem Solving Environment for Electrochemistry, 2. The Kinetic Facilities of EccoA Compiler for (Electro-)Chemistry [J. Chem. Inf. Comput. Sci 44, 2051-2060 (2004)]. 2762
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