Volume 46,
Number 1,
January 2006
Papers from the Fourth Indo-U.S. workshop on Mathematical Chemistry January 8-12,
2005,
Pune,
Maharashtra,
India
- Dilip K. Sinha, Subhash C. Basak:
Fourth Indo-U.S. Workshop on Mathematical Chemistry, January 8-12, 2005, Pune, Maharashtra, India.
1
Electronic Edition (link) BibTeX
- Matevz Pompe, Milan Randic:
"Anticonnectivity": A Challenge for Structure-Property-Activity Studies.
2-8
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Subhash Ajmani, Kamalakar Jadhav, Sudhir A. Kulkarni:
Three-Dimensional QSAR Using the k-Nearest Neighbor Method and Its Interpretation.
24-31
Electronic Edition (link) BibTeX
- Marco Pintore, Christophe Wechman, Gilles Sicard, Maurice Chastrette, Nicolas Amaury, Jacques R. Chrétien:
Comparing the Information Content of Two Large Olfactory Databases.
32-38
Electronic Edition (link) BibTeX
- Philip Prathipati, Anil K. Saxena:
Evaluation of Binary QSAR Models Derived from LUDI and MOE Scoring Functions for Structure Based Virtual Screening.
39-51
Electronic Edition (link) BibTeX
- Yenamandra S. Prabhakar, Krishnan Balasubramanian:
A Simple Algorithm for Unique Representation of Chemical Structures-Cyclic/Acyclic Functionalized Achiral Molecules.
52-56
Electronic Edition (link) BibTeX
- Milan Randic, Alexandru T. Balaban:
Partitioning of pi-Electrons in Rings for Clar Structures of Benzenoid Hydrocarbons.
57-64
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Samrat Dutta, Poonam Singhal, Praveen Agrawal, Raju Tomer, Kritee, Ekta Khurana, B. Jayaram:
A Physicochemical Model for Analyzing DNA Sequences.
78-85
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Manish K. Gupta, Yenamandra S. Prabhakar:
Topological Descriptors in Modeling the Antimalarial Activity of 4-(3', 5'-Disubstituted anilino)quinolines.
93-102
Electronic Edition (link) BibTeX
- Mamta Thakur, Abhilash Thakur, Krishnan Balasubramanian:
QSAR and SAR Studies on the Reduction of Some Aromatic Nitro Compounds by Xanthine Oxidase.
103-110
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- R. Sathyapriya, K. V. Brinda, Saraswathi Vishveshwara:
Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures.
123-129
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Chemical Information
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Zsolt Lepp, Takashi Kinoshita, Hiroshi Chuman:
Screening for New Antidepressant Leads of Multiple Activities by Support Vector Machines.
158-167
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Robert P. Sheridan, Peter Hunt, J. Christopher Culberson:
Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR.
180-192
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Andrew Smellie, Christopher J. Wilson, Shi Chung Ng:
Visualization and Interpretation of High Content Screening Data.
201-207
Electronic Edition (link) BibTeX
- Nikolaus Stiefl, Ian A. Watson, Knut Baumann, Andrea Zaliani:
ErG: 2D Pharmacophore Descriptions for Scaffold Hopping.
208-220
Electronic Edition (link) BibTeX
Computational Chemistry
- 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
Electronic Edition (link) BibTeX
- Matthew Clark, Frank Guarnieri, Igor Shkurko, Jeff Wiseman:
Grand Canonical Monte Carlo Simulation of Ligand-Protein Binding.
231-242
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Orazio Nicolotti, Angelo Carotti:
QSAR and QSPR Studies of a Highly Structured Physicochemical Domain.
264-276
Electronic Edition (link) BibTeX
- J. Christian Baber, William A. Shirley, Yinghong Gao, Miklos Feher:
The Use of Consensus Scoring in Ligand-Based Virtual Screening.
277-288
Electronic Edition (link) BibTeX
- Prabha Garg, Jitender Verma:
In Silico Prediction of Blood Brain Barrier Permeability: An Artificial Neural Network Model.
289-297
Electronic Edition (link) BibTeX
- Sung Jin Cho, Yaxiong Sun:
FLAME: A Program to Flexibly Align Molecules.
298-306
Electronic Edition (link) BibTeX
- Douglas J. Klein, Alexandru T. Balaban:
The Eight Classes of Positive-Curvature Graphitic Nanocones.
307-320
Electronic Edition (link) BibTeX
- Debojyoti Dutta, Rajarshi Guha, Peter C. Jurs, Ting Chen:
Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing.
321-333
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- Shane D. Peterson, Wesley Schaal, Anders Karlén:
Improved CoMFA Modeling by Optimization of Settings.
355-364
Electronic Edition (link) BibTeX
- Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson:
Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study.
365-379
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Minghu Song, Matthew Clark:
Development and Evaluation of an in Silico Model for hERG Binding.
392-400
Electronic Edition (link) BibTeX
- Hongming Chen, Paul D. Lyne, Fabrizio Giordanetto, Timothy Lovell, Jin Li:
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors.
401-415
Electronic Edition (link) BibTeX
- Tomasz Arodz, David A. Yuen, Arkadiusz Z. Dudek:
Ensemble of Linear Models for Predicting Drug Properties.
416-423
Electronic Edition (link) BibTeX
- Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, Thomas Lengauer:
A Fully Computational Model for Predicting Percutaneous Drug Absorption.
424-429
Electronic Edition (link) BibTeX
Bioinformatics
Software Description
Volume 46,
Number 2,
March 2006
Papers from the Seventh International Conference on Chemical Structures,
Noordwijkerhout,
the Netherlands,
June 2005
Articles
- Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender:
Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme.
452-461
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- David J. Wilton, Robert F. Harrison, Peter Willett, John Delaney, Kevin Lawson, Graham Mullier:
Virtual Screening Using Binary Kernel Discrimination: Analysis of Pesticide Data.
471-477
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- David J. Wild, Gary Wiggins:
Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University.
495-502
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Mireille Krier, Guillaume Bret, Didier Rognan:
Assessing the Scaffold Diversity of Screening Libraries.
512-524
Electronic Edition (link) BibTeX
- Ansgar Schuffenhauer, Nathan Brown, Paul Selzer, Peter Ertl, Edgar Jacoby:
Relationships between Molecular Complexity, Biological Activity, and Structural Diversity.
525-535
Electronic Edition (link) BibTeX
- Modest von Korff, Thomas Sander:
Toxicity-Indicating Structural Patterns.
536-544
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- György Pirok, Nóra Máté, Jeno Varga, József Szegezdi, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia:
Making "Real" Molecules in Virtual Space.
563-568
Electronic Edition (link) BibTeX
- Sarah Rodgers, Robert C. Glen, Andreas Bender:
Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model.
569-576
Electronic Edition (link) BibTeX
- Kristian Birchall, Valerie J. Gillet, Gavin Harper, Stephen D. Pickett:
Training Similarity Measures for Specific Activities: Application to Reduced Graphs.
577-586
Electronic Edition (link) BibTeX
- Nikolaus Stiefl, Andrea Zaliani:
A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening.
587-596
Electronic Edition (link) BibTeX
- Jeroen Kazius, Siegfried Nijssen, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman:
Substructure Mining Using Elaborate Chemical Representation.
597-605
Electronic Edition (link) BibTeX
- Ingrid M. Socorro, Jonathan M. Goodman:
The ROBIA Program for Predicting Organic Reactivity.
606-614
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Pekka T. Lehtovuori, Tommi H. Nyrönen:
SOMA - Workflow for Small Molecule Property Calculations on a Multiplatform Computing Grid.
620-625
Electronic Edition (link) BibTeX
- Dumitru Erhan, Pierre-Jean L'Heureux, Shi Yi Yue, Yoshua Bengio:
Collaborative Filtering on a Family of Biological Targets.
626-635
Electronic Edition (link) BibTeX
- Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
Model Selection Based on Structural Similarity-Method Description and Application to Water Solubility Prediction.
636-641
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Tim Cheeseright, Mark Mackey, Sally Rose, Andy Vinter:
Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation.
665-676
Electronic Edition (link) BibTeX
- Markus Wagener, Jos P. M. Lommerse:
The Quest for Bioisosteric Replacements.
677-685
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Uli Fechner, Gisbert Schneider:
Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design.
699-707
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nicola D. Gold, Richard M. Jackson:
A Searchable Database for Comparing Protein-Ligand Binding Sites for the Analysis of Structure-Function Relationships.
736-742
Electronic Edition (link) BibTeX
- Linda Hirons, Eleanor J. Gardiner, Christopher A. Hunter, Peter Willett:
Structural DNA Profiles: Single Sequence Queries.
743-752
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Joseph L. Durant, Burton A. Leland, James G. Nourse:
VET: A Tool for Reaction Plausibility Checking.
762-766
Electronic Edition (link) BibTeX
Chemical Information
- A. Ben Wagner:
SciFinder Scholar 2006: An Empirical Analysis of Research Topic Query Processing.
767-774
Electronic Edition (link) BibTeX
- Hideyuki Masui, Huixiao Hong:
Spec2D: A Structure Elucidation System Based on 1H NMR and H-H COSY Spectra in Organic Chemistry.
775-787
Electronic Edition (link) BibTeX
- Jerry Ray Dias:
What Do We Know about C28H14 and C30H14 Benzenoid Hydrocarbons and Their Evolution to Related Polymer Strips?.
788-800
Electronic Edition (link) BibTeX
- Jenna L. Wang, Paul G. Mezey:
The Electronic Structures and Properties of Open-Ended and Capped Carbon Nanoneedles.
801-807
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- W. Michael Brown, Shawn Martin, Mark D. Rintoul, Jean-Loup Faulon:
Designing Novel Polymers with Targeted Properties Using the Signature Molecular Descriptor.
826-835
Electronic Edition (link) BibTeX
- David Vidal, Michael Thormann, Miquel Pons:
A Novel Search Engine for Virtual Screening of Very Large Databases.
836-843
Electronic Edition (link) BibTeX
Computational Chemistry
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Rainer Brüggemann, Guillermo Restrepo, Kristina Voigt:
Structure-Fate Relationships of Organic Chemicals Derived from the Software Packages E4CHEM and WHASSE.
894-902
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Natalie Fey, Stephanie E. Harris, Jeremy N. Harvey, A. Guy Orpen:
Adding Value to Crystallographically-Derived Knowledge Bases.
912-929
Electronic Edition (link) BibTeX
Pharmaceutical Modeling
Volume 46,
Number 3,
May 2006
Editorial
Articles
- 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
Electronic Edition (link) BibTeX
- Sulev Sild, Uko Maran, Andre Lomaka, Mati Karelson:
Open Computing Grid for Molecular Science and Engineering.
953-959
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Thanh N. Truong, Manohar Nayak, Hung H. Huynh, Tom Cook, Priya Mahajan, LeThuy 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
Electronic Edition (link) BibTeX
- Henry S. Rzepa, Andrew Wheat, Mark J. Williamson:
ChemSem: An Extensible and Scalable RSS-Based Seminar Alerting System for Scientific Collaboration.
985-990
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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 Lyon, Rachel Heery, Monica Duke, Michael Day:
An E-Science Environment for Service Crystallography-from Submission to Dissemination.
1006-1016
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Matt J. Harvey, D. Scott, Peter V. Coveney:
An Integrated Instrument Control and Informatics System for Combinatorial Materials Research.
1026-1033
Electronic Edition (link) BibTeX
- Peter Lind, Markus Alm:
A Database-Centric Virtual Chemistry System.
1034-1039
Electronic Edition (link) BibTeX
Chemical Information
- Michael Thormann, Andreas Klamt, Martin Hornig, Michael Almstetter:
COSMOsim: Bioisosteric Similarity Based on COSMO-RS sigma Profiles.
1040-1053
Electronic Edition (link) BibTeX
- Fumiyoshi Yamashita, Takayuki Itoh, Hideto Hara, Mitsuru Hashida:
Visualization of Large-Scale Aqueous Solubility Data Using a Novel Hierarchical Data Visualization Technique.
1054-1059
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Surjit B. Dixit, Sergei Y. Ponomarev, David L. Beveridge:
Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA.
1084-1093
Electronic Edition (link) BibTeX
- Jeffrey W. Godden, Jürgen Bajorath:
A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations.
1094-1097
Electronic Edition (link) BibTeX
- Dariusz Plewczynski, Stéphane A. H. Spieser, Uwe Koch:
Assessing Different Classification Methods for Virtual Screening.
1098-1106
Electronic Edition (link) BibTeX
- Alex M. Clark, Paul Labute, Martin Santavy:
2D Structure Depiction.
1107-1123
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Computational Chemistry
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Laleh Alisaraie, Lars A. Haller, Gregor Fels:
A QXP-Based Multistep Docking Procedure for Accurate Prediction of Protein-Ligand Complexes.
1174-1187
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Milan Remko, Claus-Wilhelm von der Lieth:
Gas-Phase and Solution Conformations of the alpha-L-Iduronic Acid Structural Unit of Heparin.
1194-1200
Electronic Edition (link) BibTeX
- Thierry Kogej, Ola Engkvist, Niklas Blomberg, Sorel Muresan:
Multifingerprint Based Similarity Searches for Targeted Class Compound Selection.
1201-1213
Electronic Edition (link) BibTeX
- Artem Cherkasov:
Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?.
1214-1222
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha:
Combinatorial QSAR Modeling of P-Glycoprotein Substrates.
1245-1254
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- 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
Electronic Edition (link) BibTeX
- Munikumar R. Doddareddy, Yong Seo Cho, Hun Yeong Koh, Dong Hyun Kim, Ae Nim Pae:
In Silico Renal Clearance Model Using Classical Volsurf Approach.
1312-1320
Electronic Edition (link) BibTeX
- Tulay Ercanli, Donald B. Boyd:
Exploration of the Conformational Space of a Polymeric Material that Inhibits Human Immunodeficiency Virus.
1321-1333
Electronic Edition (link) BibTeX
- Micael Jacobsson, Anders Karlén:
Ligand Bias of Scoring Functions in Structure-Based Virtual Screening.
1334-1343
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jun Feng, Ashish P. Sanil, S. Stanley Young:
PharmID: Pharmacophore Identification Using Gibbs Sampling.
1352-1359
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Katsumi Yoshida, Tomoko Niwa:
Quantitative Structure-Activity Relationship Studies on Inhibition of HERG Potassium Channels.
1371-1378
Electronic Edition (link) BibTeX
- Pierre Bruneau, Nathan R. McElroy:
logD7.4 Modeling Using Bayesian Regularized Neural Networks. Assessment and Correction of the Errors of Prediction.
1379-1387
Electronic Edition (link) BibTeX
- Xavier Gironés, Robert Ponec:
Molecular Quantum Similarity Measures from Fermi Hole Densities: Modeling Hammett Sigma Constants.
1388-1393
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Sven Serneels, Evert De Nolf, Pierre J. Van Espen:
Spatial Sign Preprocessing: A Simple Way To Impart Moderate Robustness to Multivariate Estimators.
1402-1409
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Máté Dervarics, Ferenc Ötvös, Tamás A. Martinek:
Development of a Chirality-Sensitive Flexibility Descriptor for 3+3D-QSAR.
1431-1438
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Markus H. J. Seifert:
Assessing the Discriminatory Power of Scoring Functions for Virtual Screening.
1456-1465
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Bioinformatics
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- M. Michael Gromiha, Samuel Selvaraj, A. Mary Thangakani:
A Statistical Method for Predicting Protein Unfolding Rates from Amino Acid Sequence.
1503-1508
Electronic Edition (link) BibTeX
- Dimitri Gilis:
In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic alpha-Amylases upon Exhaustive Single-Site Mutations.
1509-1516
Electronic Edition (link) BibTeX
Software Description
Volume 46,
Number 4,
July 2006
Editorial
Articles - Chemical Information
- Jean-François Truchon, Christopher I. Bayly:
GLARE: A New Approach for Filtering Large Reagent Lists in Combinatorial Library Design Using Product Properties.
1536-1548
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Alexandru T. Balaban, Thomas G. Schmalz:
Strain-Free Sextet-Resonant Benzenoids and Their Antisextet Dualists.
1563-1579
Electronic Edition (link) BibTeX
- Modest von Korff, Kurt Hilpert:
Assessing the Predictive Power of Unsupervised Visualization Techniques to Improve the Identification of GPCR-Focused Compound Libraries.
1580-1587
Electronic Edition (link) BibTeX
- Sara H. Fitzgerald, Michal Sabat, H. Mario Geysen:
Diversity Space and Its Application to Library Selection and Design.
1588-1597
Electronic Edition (link) BibTeX
- Aleksandr Y. Sedykh, Gilles Klopman:
A Structural Analogue Approach to the Prediction of the Octanol-Water Partition Coefficient.
1598-1603
Electronic Edition (link) BibTeX
- Thy-Hou Lin, Shih-Hau Chiu, Keng-Chang Tsai:
Supervised Feature Ranking Using a Genetic Algorithm Optimized Artificial Neural Network.
1604-1614
Electronic Edition (link) BibTeX
- Elisabet Gregori-Puigjané, Jordi Mestres:
SHED: Shannon Entropy Descriptors from Topological Feature Distributions.
1615-1622
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Computational Chemistry
- Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher:
SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions.
1635-1642
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Manuel Urbano-Cuadrado, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
A Steroids QSAR Approach Based on Approximate Similarity Measurements.
1678-1686
Electronic Edition (link) BibTeX
- Milan Remko, Claus-Wilhelm von der Lieth:
Gas-Phase and Solution Conformations of Selected Dimeric Structural Units of Heparin.
1687-1694
Electronic Edition (link) BibTeX
- Andreas Steffen, Andreas Kämper, Thomas Lengauer:
Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm.
1695-1703
Electronic Edition (link) BibTeX
- Stéphane Betzi, Karsten Suhre, Bernard Chétrit, Françoise Guerlesquin, Xavier Morelli:
GFscore: A General Nonlinear Consensus Scoring Function for High-Throughput Docking.
1704-1712
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Paul Laffort, Pierre Héricourt:
Solvation Parameters. 2. A Simplified Molecular Topology to Generate Easily Optimized Values.
1723-1734
Electronic Edition (link) BibTeX
- Michael H. Abraham, Adam Ibrahim:
Gas to Olive Oil Partition Coefficients: A Linear Free Energy Analysis.
1735-1741
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- 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
Electronic Edition (link) BibTeX
- Tímea Polgár, György M. Keserü:
Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase.
1795-1805
Electronic Edition (link) BibTeX
- Dharmesh M. Maniyar, Ian T. Nabney, Bruce S. Williams, Andreas Sewing:
Data Visualization during the Early Stages of Drug Discovery.
1806-1818
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Rajarshi Guha, Debojyoti Dutta, Peter C. Jurs, Ting Chen:
Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions.
1836-1847
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Software Description
Bioinformatics
Copyright © Sun May 17 00:07:41 2009
by Michael Ley (ley@uni-trier.de)
