Volume 45,
Number 1,
January 2005
Editorial
Articles - Chemical Information
Computational Chemistry
- Zhenming Liu, Changkang Huang, Keqiang Fan, Ping Wei, Hao Chen, Shiyong Liu, Jianfeng Pei, Lei Shi, Bo Li, Kun Yang, Ying Liu, Luhua Lai:
Virtual Screening of Novel Noncovalent Inhibitors for SARS-CoV 3C-like Proteinase.
10-17
Electronic Edition (link) BibTeX
- Tomasz Spalek, Piotr Pietrzyk, Zbigniew Sojka:
Application of the Genetic Algorithm Joint with the Powell Method to Nonlinear Least-Squares Fitting of Powder EPR Spectra.
18-29
Electronic Edition (link) BibTeX
- Matthew Clark:
Generalized Fragment-Substructure Based Property Prediction Method.
30-38
Electronic Edition (link) BibTeX
- Jaroslaw J. Panek, Aneta Jezierska, Krzysztof Mierzwicki, Zdzislaw Latajka, Aleksander Koll:
Molecular Modeling Study of Leflunomide and Its Active Metabolite Analogues.
39-48
Electronic Edition (link) BibTeX
- Karthigeyan Nagarajan, Randy J. Zauhar, William J. Welsh:
Enrichment of Ligands for the Serotonin Receptor Using the Shape Signatures Approach.
49-57
Electronic Edition (link) BibTeX
- Sasa Kovacic, Antonija Lesar, Milan Hodoscek:
Quantum Mechanical Study of the Potential Energy Surface of the ClO + NO2 Reaction.
58-64
Electronic Edition (link) BibTeX
- Rajarshi Guha, Peter C. Jurs:
Determining the Validity of a QSAR Model - A Classification Approach.
65-73
Electronic Edition (link) BibTeX
- Christoph Rücker, Markus Meringer, Adalbert Kerber:
QSPR Using MOLGEN-QSPR: The Challenge of Fluoroalkane Boiling Points.
74-80
Electronic Edition (link) BibTeX
- K. M. Nalin de Silva, Jonathan M. Goodman:
What Is the Smallest Saturated Acyclic Alkane that Cannot Be Made?.
81-87
Electronic Edition (link) BibTeX
- Wei Zhang, Tingjun Hou, Xiaojie Xu:
New Born Radii Deriving Method for Generalized Born Model.
88-93
Electronic Edition (link) BibTeX
- Iiris Kahn, Dan C. Fara, Mati Karelson, Uko Maran, Patrik L. Andersson:
QSPR Treatment of the Soil Sorption Coefficients of Organic Pollutants.
94-105
Electronic Edition (link) BibTeX
Computational Biochemistry
- Tatiana I. Netzeva, Aynur O. Aptula, Emilio Benfenati, Mark T. D. Cronin, Giuseppina C. Gini, Iglika Lessigiarska, Uko Maran, Marjan Vracko, Gerrit Schüürmann:
Description of the Electronic Structure of Organic Chemicals Using Semiempirical and Ab Initio Methods for Development of Toxicological QSARs.
106-114
Electronic Edition (link) BibTeX
- Chun Li, Jun Wang:
New Invariant of DNA Sequences.
115-120
Electronic Edition (link) BibTeX
- Huabei Zhang:
A New Approach for the Tissue-Blood Partition Coefficients of Neutral and Ionized Compounds.
121-127
Electronic Edition (link) BibTeX
- Edward J. Bertaccini, Jessica Shapiro, Douglas L. Brutlag, James R. Trudell:
Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site.
128-135
Electronic Edition (link) BibTeX
- Philip Prathipati, Gyanendra Pandey, Anil K. Saxena:
CoMFA and Docking Studies on Glycogen Phosphorylase a Inhibitors as Antidiabetic Agents.
136-145
Electronic Edition (link) BibTeX
- Eva M. Krovat, Karin H. Frühwirth, Thierry Langer:
Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa.
146-159
Electronic Edition (link) BibTeX
Pharmaceutical Modeling
Bioinformatics
Software Review
Volume 45,
Number 2,
March 2005
Articles - Chemical Information
- Paul Labute:
On the Perception of Molecules from 3D Atomic Coordinates.
215-221
Electronic Edition (link) BibTeX
- Ivan Gutman, Pierre Hansen, Hadrien Mélot:
Variable Neighborhood Search for Extremal Graphs. 10. Comparison of Irregularity Indices for Chemical Trees.
222-230
Electronic Edition (link) BibTeX
- Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto, Juan Antonio Cabrero Doncel, Antonio Guevara Plaza:
From Wiener Index to Molecules.
231-238
Electronic Edition (link) BibTeX
- Stephan C. Schürer, Prashant Tyagi, Steven M. Muskal:
Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space.
239-248
Electronic Edition (link) BibTeX
- Klaus-Robert Müller, Gunnar Rätsch, Sören Sonnenburg, Sebastian Mika, Michael Grimm, Nikolaus Heinrich:
Classifying 'Drug-likeness' with Kernel-Based Learning Methods.
249-253
Electronic Edition (link) BibTeX
Computational Chemistry
- Youngyong In, Han Ha Chai, Kyoung Tai No:
A Partition Coefficient Calculation Method with the SFED Model.
254-263
Electronic Edition (link) BibTeX
- Jaroslaw J. Panek, Aneta Jezierska, Marjan Vracko:
Kohonen Network Study of Aromatic Compounds Based on Electronic and Nonelectronic Structure Descriptors.
264-272
Electronic Edition (link) BibTeX
- Michael E. Beck:
Do Fukui Function Maxima Relate to Sites of Metabolism? A Critical Case Study.
273-282
Electronic Edition (link) BibTeX
- Ovanes Mekenyan, Todor Pavlov, Vanjo Grancharov, Milen Todorov, Patricia Schmieder, Gilman Veith:
2D-3D Migration of Large Chemical Inventories with Conformational Multiplication. Application of the Genetic Algorithm.
283-292
Electronic Edition (link) BibTeX
- Mircea V. Diudea, Csaba L. Nagy, Ioan Silaghi-Dumitrescu, Ante Graovac, Dusanka Janezic, Drazen Vikic-Topic:
Periodic Cages.
293-299
Electronic Edition (link) BibTeX
- Kitiyaporn Wittayanarakul, Ornjira Aruksakunwong, Pornthep Sompornpisut, Vannajan Sanghiran-Lee, Vudhichai Parasuk, Surapong Pinitglang, Supot Hannongbua:
Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance: Molecular Dynamic Simulations.
300-308
Electronic Edition (link) BibTeX
- Jure Zupan, Milan Randic:
Algorithm for Coding DNA Sequences into "Spectrum-like" and "Zigzag" Representations.
309-313
Electronic Edition (link) BibTeX
- Nikolay P. Todorov, Christoph L. Buenemann, Ian L. Alberts:
Combinatorial Ligand Design Targeted at Protein Families.
314-320
Electronic Edition (link) BibTeX
- Anna Gallegos, Xavier Gironés:
Topological Quantum Similarity Indices Based on Fitted Densities: Theoretical Background and QSPR Application.
321-326
Electronic Edition (link) BibTeX
- Ivo Cacelli, Silvio Campanile, Alessandro Giolitti, Dafne Molin:
Theoretical Prediction of the Abraham Hydrogen Bond Acidity and Basicity Factors from a Reaction Field Method.
327-333
Electronic Edition (link) BibTeX
- Igor Novak:
Molecular Modeling of Anti-Bredt Compounds.
334-338
Electronic Edition (link) BibTeX
- Orsolya Farkas, Károly Héberger:
Comparison of Ridge Regression, Partial Least-Squares, Pairwise Correlation, Forward- and Best Subset Selection Methods for Prediction of Retention Indices for Aliphatic Alcohols.
339-346
Electronic Edition (link) BibTeX
- Qishi Du, Peng-Jun Liu, Paul G. Mezey:
Theoretical Derivation of Heuristic Molecular Lipophilicity Potential: A Quantum Chemical Description for Molecular Solvation.
347-353
Electronic Edition (link) BibTeX
- Norberto Castillo, Chérif F. Matta, Russell J. Boyd:
Fluorine-Fluorine Spin-Spin Coupling Constants in Aromatic Compounds: Correlations with the Delocalization Index and with the Internuclear Separation.
354-359
Electronic Edition (link) BibTeX
- Laura K. Schnackenberg, Richard D. Beger:
Whole-Molecule Calculation of Log P Based on Molar Volume, Hydrogen Bonds, and Simulated 13C NMR Spectra.
360-365
Electronic Edition (link) BibTeX
- Marjan A. Rafiee, Nasser L. Hadipour, Hossein Naderi-manesh:
The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues.
366-370
Electronic Edition (link) BibTeX
- Fei Cai, Heqing Shao, Chungen Liu, Yuansheng Jiang:
An Alternative Strategy for Count and Storage of Kekulé and Longer Range Resonance Valence Bond Structures.
371-378
Electronic Edition (link) BibTeX
Computational Biochemistry
- Martin Smiesko, Emilio Benfenati:
Thermodynamic Descriptors Derived from Density Functional Theory Calculations in Prediction of Aquatic Toxicity.
379-385
Electronic Edition (link) BibTeX
- David Vidal, Michael Thormann, Miquel Pons:
LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities.
386-393
Electronic Edition (link) BibTeX
- Janez Strancar, Tilen Koklic, Zoran Arsov, Bogdan Filipic, David Stopar, Marcus A. Hemminga:
Spin Label EPR-Based Characterization of Biosystem Complexity.
394-406
Electronic Edition (link) BibTeX
- Kuo-Chen Chou, Yu-Dong Cai:
Prediction of Membrane Protein Types by Incorporating Amphipathic Effects.
407-413
Electronic Edition (link) BibTeX
- Christian Hofbauer, András Aszódi:
SH2 Binding Site Comparison: A New Application of the SURFCOMP Method.
414-421
Electronic Edition (link) BibTeX
Pharmaceutical Modeling
- Johannes Kirchmair, Christian Laggner, Gerhard Wolber, Thierry Langer:
Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms.
422-430
Electronic Edition (link) BibTeX
- Daniela Schuster, Thierry Langer:
The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling.
431-439
Electronic Edition (link) BibTeX
- Huabei Zhang, Hua Li, Chunping Liu:
CoMFA, CoMSIA, and Molecular Hologram QSAR Studies of Novel Neuronal nAChRs Ligands-Open Ring Analogues of 3-Pyridyl Ether.
440-448
Electronic Edition (link) BibTeX
- Markus H. J. Seifert:
ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment.
449-460
Electronic Edition (link) BibTeX
- Rajendra Kristam, Valerie J. Gillet, Richard A. Lewis, David A. Thorner:
Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst.
461-476
Electronic Edition (link) BibTeX
- Bernard Pirard, Joachim Brendel, Stefan Peukert:
The Discovery of Kv1.5 Blockers as a Case Study for the Application of Virtual Screening Approaches.
477-485
Electronic Edition (link) BibTeX
Bioinformatics
Software Description
Errata
Volume 45,
Number 3,
May 2005
Articles Chemical Information
Computational Chemistry
- Muthukumarasamy Karthikeyan, Robert C. Glen, Andreas Bender:
General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks.
581-590
Electronic Edition (link) BibTeX
- Tulay Ercanli, Donald B. Boyd:
Evaluation of Computational Chemistry Methods: Crystallographic and Cheminformatics Analysis of Aminothiazole Methoximes.
591-601
Electronic Edition (link) BibTeX
- Stefano Alcaro, Francesco Ortuso, Robert S. Coleman:
Molecular Modeling of DNA Cross-linking Analogues Based on the Azinomycin Scaffold.
602-609
Electronic Edition (link) BibTeX
- Milind Misra, Amit Banerjee, Rajesh N. Davé, Carol A. Venanzi:
Novel Feature Extraction Technique for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor.
610-623
Electronic Edition (link) BibTeX
- Alfonso T. García-Sosa, Stuart Firth-Clark, Ricardo L. Mancera:
Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplification through the in Silico Generation of Poly(ADP-ribose)polymerase Ligands.
624-633
Electronic Edition (link) BibTeX
- Filip Fratev, Emilio Benfenati:
3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones.
634-644
Electronic Edition (link) BibTeX
- Alessandra R. Rufino, Antônio J. C. Brant, João B. O. Santos, Marcelo J. P. Ferreira, Vicente de Paulo Emerenciano:
Simple Method for Identification of Skeletons of Aporphine Alkaloids from 13C NMR Data Using Artificial Neural Networks.
645-651
Electronic Edition (link) BibTeX
- Tadeusz Marek Krygowski, Halina Szatylowicz, Joanna E. Zachara:
Molecular Geometry as a Source of Chemical Information. 5. Substituent Effect on Proton Transfer in Para-Substituted Phenol Complexes with Fluoride-a B3LYP/6-311+G** Study.
652-656
Electronic Edition (link) BibTeX
- Yegor Zyrianov:
Distribution-Based Descriptors of the Molecular Shape.
657-672
Electronic Edition (link) BibTeX
- James A. Haigh, Barry T. Pickup, J. Andrew Grant, Anthony Nicholls:
Small Molecule Shape-Fingerprints.
673-684
Electronic Edition (link) BibTeX
- Philippe Vismara, Yannic S. Tognetti, Claude Laurenço:
Maximum Symmetrical Split of Molecular Graphs. Application to Organic Synthesis Design.
685-695
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- Elodie Lescot, Ronan Bureau, Jana Sopkova-de Oliveira Santos, Christophe Rochais, Vincent Lisowski, Jean-Charles Lancelot, Sylvain Rault:
3D-QSAR and Docking Studies of Selective GSK-3beta Inhibitors. Comparison with a Thieno[2, 3-b]pyrrolizinone Derivative, a New Potential Lead for GSK-3beta Ligands.
708-715
Electronic Edition (link) BibTeX
- Theodora M. Steindl, Christian Laggner, Thierry Langer:
Human Rhinovirus 3C Protease: Generation of Pharmacophore Models for Peptidic and Nonpeptidic Inhibitors and Their Application in Virtual Screening.
716-724
Electronic Edition (link) BibTeX
- Vema Aparna, G. Rambabu, Sunil K. Panigrahi, J. A. R. P. Sarma, Gautam R. Desiraju:
Virtual Screening of 4-Anilinoquinazoline Analogues as EGFR Kinase Inhibitors: Importance of Hydrogen Bonds in the Evaluation of Poses and Scoring Functions.
725-738
Electronic Edition (link) BibTeX
- Nikolaus Stiefl, Knut Baumann:
Structure-Based Validation of the 3D-QSAR Technique MaP.
739-749
Electronic Edition (link) BibTeX
- Yong-Hua Wang, Yan Li, Sheng-Li Yang, Ling Yang:
Classification of Substrates and Inhibitors of P-Glycoprotein Using Unsupervised Machine Learning Approach.
750-757
Electronic Edition (link) BibTeX
- Céline Le Bailly de Tilleghem, Benoît Beck, Bruno Boulanger, Bernadette Govaerts:
A Fast Exchange Algorithm for Designing Focused Libraries in Lead Optimization.
758-767
Electronic Edition (link) BibTeX
- T. John McNeany, Jonathan D. Hirst:
Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Nonparametric Regression.
768-776
Electronic Edition (link) BibTeX
- Peter Itskowitz, Alexander Tropsha:
k Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications.
777-785
Electronic Edition (link) BibTeX
- Vladimir Svetnik, Ting Wang, Christopher Tong, Andy Liaw, Robert P. Sheridan, Qinghua Song:
Boosting: An Ensemble Learning Tool for Compound Classification and QSAR Modeling.
786-799
Electronic Edition (link) BibTeX
Bioinformatics
Volume 45,
Number 4,
July 2005
Articles Chemical Information
- Alexander Böcker, Swetlana Derksen, Elena Schmidt, Andreas Teckentrup, Gisbert Schneider:
A Hierarchical Clustering Approach for Large Compound Libraries.
807-815
Electronic Edition (link) BibTeX
- Michael Frenkel, Robert D. Chirico, Vladimir V. Diky, Xinjian Yan, Qian Dong, Chris Muzny:
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept.
816-838
Electronic Edition (link) BibTeX
- Sabcho Dimitrov, Gergana Dimitrova, Todor Pavlov, Nadezhda Dimitrova, Grace Patlewicz, Jay Niemela, Ovanes Mekenyan:
A Stepwise Approach for Defining the Applicability Domain of SAR and QSAR Models.
839-849
Electronic Edition (link) BibTeX
- Lijie Wang, Peter Warburton, Zsolt Szekeres, Peter Surjan, Paul G. Mezey:
Stability and Properties of Polyhelicenes and Annelated Fused-Ring Carbon Helices: Models Toward Helical Graphites.
850-855
Electronic Edition (link) BibTeX
- Suxin Zheng, Xiaomin Luo, Gang Chen, Weiliang Zhu, Jianhua Shen, Kaixian Chen, Hualiang Jiang:
A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database.
856-862
Electronic Edition (link) BibTeX
- Robin Hewitt, Alberto Gobbi, Man-Ling Lee:
A Searching and Reporting System for Relational Databases Using a Graph-Based Metadata Representation.
863-869
Electronic Edition (link) BibTeX
- Teodora Ivanciuc, Ovidiu Ivanciuc, Douglas J. Klein:
Posetic Quantitative Superstructure/Activity Relationships (QSSARs) for Chlorobenzenes.
870-879
Electronic Edition (link) BibTeX
Computational Chemistry
- Peter Zinn:
Adaptive Multicomponent Analysis by Genetic Algorithms.
880-887
Electronic Edition (link) BibTeX
- Sorel Muresan, Jens Sadowski:
"In-House Likeness": Comparison of Large Compound Collections Using Artificial Neural Networks.
888-893
Electronic Edition (link) BibTeX
- César Hervás-Martínez, Alfonso Carlos Martínez, Manuel Silva, Juan Manuel Serrano:
Improving the Quantification of Highly Overlapping Chromatographic Peaks by Using Product Unit Neural Networks Modeled by an Evolutionary Algorithm.
894-903
Electronic Edition (link) BibTeX
- Frances V. Buontempo, Xue Zhong Wang, Mulaisho Mwense, Nigel Horan, Anita Young, Daniel Osborn:
Genetic Programming for the Induction of Decision Trees to Model Ecotoxicity Data.
904-912
Electronic Edition (link) BibTeX
- Alan R. Katritzky, Indrek Tulp, Dan C. Fara, Antonino Lauria, Uko Maran, William E. Acree Jr.:
A General Treatment of Solubility. 3. Principal Component Analysis (PCA) of the Solubilities of Diverse Solutes in Diverse Solvents.
913-923
Electronic Edition (link) BibTeX
- Matthew D. Miller, David M. Yourtee, Alan G. Glaros, Cecil C. Chappelow, J. David Eick, Andrew J. Holder:
Quantum Mechanical Structure-Activity Relationship Analyses for Skin Sensitization.
924-929
Electronic Edition (link) BibTeX
- Milan Soskic, Dejan Plavsic:
Modeling the Octanol-Water Partition Coefficients by an Optimized Molecular Connectivity Index.
930-938
Electronic Edition (link) BibTeX
- Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert:
Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines.
939-951
Electronic Edition (link) BibTeX
- Shengqiao Li, Adam Fedorowicz, Harshinder Singh, Sidney C. Soderholm:
Application of the Random Forest Method in Studies of Local Lymph Node Assay Based Skin Sensitization Data.
952-964
Electronic Edition (link) BibTeX
- Corneliu Buda, Abul B. Kazi, Adriana Dinescu, Thomas R. Cundari:
Stability Studies of Transition-Metal Linkage Isomers Using Quantum Mechanical Methods. Groups 11 and 12 Transition Metals.
965-970
Electronic Edition (link) BibTeX
- James L. Melville, Kevin R. J. Lovelock, Claire Wilson, Bryan Allbutt, Edmund K. Burke, Barry Lygo, Jonathan D. Hirst:
Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships.
971-981
Electronic Edition (link) BibTeX
- Chun Wei Yap, Yu Zong Chen:
Prediction of Cytochrome P450 3A4, 2D6, and 2C9 Inhibitors and Substrates by Using Support Vector Machines.
982-992
Electronic Edition (link) BibTeX
- Simon S. J. Cross:
Improved FlexX Docking Using FlexS-Determined Base Fragment Placement.
993-1001
Electronic Edition (link) BibTeX
- Mircea V. Diudea:
Nanoporous Carbon Allotropes by Septupling Map Operations.
1002-1009
Electronic Edition (link) BibTeX
- Jr-Hung Lin, Timothy Clark:
Nanoporous Carbon Allotropes by Septupling Map Operations.
1010-1016
Electronic Edition (link) BibTeX
- Vladimir N. Maiorov, Robert P. Sheridan:
Enhanced Virtual Screening by Combined Use of Two Docking Methods: Getting the Most on a Limited Budget.
1017-1023
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- Harald Mauser, Olivier Roche, Martin Stahl, Stephan Müller:
Prediction of UV and ESI-MS Signal Intensities.
1039-1046
Electronic Edition (link) BibTeX
- Brian S. Henriksen, Todd J. Zahn, Jeffrey D. Evanseck, Steven M. Firestine, Richard A. Gibbs:
Computational and Conformational Evaluation of FTase Alternative Substrates: Insight into a Novel Enzyme Binding Pocket.
1047-1052
Electronic Edition (link) BibTeX
- Bernd Ehresmann, Marcel J. de Groot, Timothy Clark:
Surface-Integral QSPR Models: Local Energy Properties.
1053-1060
Electronic Edition (link) BibTeX
- Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Daniel L. Ormsby, Mika K. Lindvall:
Retrospective Docking Study of PDE4B Ligands and an Analysis of the Behavior of Selected Scoring Functions.
1061-1074
Electronic Edition (link) BibTeX
- Alban Lepailleur, Ronan Bureau, Magalie Paillet-Loilier, Frédéric Fabis, Nicolas Saettel, Stéphane Lemaître, François Dauphin, Aurélien Lesnard, Jean-Charles Lancelot, Sylvain Rault:
Molecular Modeling Studies Focused on 5-HT7 versus 5-HT1A Selectivity. Discovery of Novel Phenylpyrrole Derivatives with High Affinity for 5-HT7 Receptors.
1075-1081
Electronic Edition (link) BibTeX
- Yovani Marrero-Ponce, Maité Iyarreta-Veitía, Alina Montero-Torres, Carlos Romero-Zaldivar, Carlos A. Brandt, Priscilla E. Ávila, Karin Kirchgatter, Yanetsy Machado:
Ligand-Based Virtual Screening and in Silico Design of New Antimalarial Compounds Using Nonstochastic and Stochastic Total and Atom-Type Quadratic Maps.
1082-1100
Electronic Edition (link) BibTeX
- B. Gopalakrishnan, V. Aparna, J. Jeevan, M. Ravi, G. R. Desiraju:
A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models.
1101-1108
Electronic Edition (link) BibTeX
- Rajarshi Guha, David T. Stanton, Peter C. Jurs:
Interpreting Computational Neural Network Quantitative Structure-Activity Relationship Models: A Detailed Interpretation of the Weights and Biases.
1109-1121
Electronic Edition (link) BibTeX
- Jamal C. Saeh, Paul D. Lyne, Bryan K. Takasaki, David A. Cosgrove:
Lead Hopping Using SVM and 3D Pharmacophore Fingerprints.
1122-1133
Electronic Edition (link) BibTeX
Bioinformatics
Volume 45,
Number 5,
September 2005
Articles Chemical Information
- Boris L. Milman:
Literature-Based Generation of Hypotheses on Chemical Composition Using Database Co-occurrence of Chemical Compounds.
1153-1158
Electronic Edition (link) BibTeX
- Christian Merkwirth, Thomas Lengauer:
Automatic Generation of Complementary Descriptors with Molecular Graph Networks.
1159-1168
Electronic Edition (link) BibTeX
- Martin Hornig, Andreas Klamt:
COSMOfrag: A Novel Tool for High-Throughput ADME Property Prediction and Similarity Screening Based on Quantum Chemistry.
1169-1177
Electronic Edition (link) BibTeX
- Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto:
Clustering Chemical Databases Using Adaptable Projection Cells and MCS Similarity Values.
1178-1194
Electronic Edition (link) BibTeX
- John W. Raymond, Christopher E. Kibbey:
An Automated Method for Exploring Targeted Substructural Diversity within Sets of Chemical Structures.
1195-1204
Electronic Edition (link) BibTeX
- Milan Randic, Marjana Novic, Marjan Vracko:
Novel Characterization of Proteomics Maps by Sequential Neighborhoods of Protein Spots.
1205-1213
Electronic Edition (link) BibTeX
- Qian Zhu, Jianhua Yao, Shengang Yuan, Feng Li, Haifeng Chen, Wei Cai, Quan Liao:
Superstructure Searching Algorithm for Generic Reaction Retrieval.
1214-1222
Electronic Edition (link) BibTeX
- Daniel J. Graham:
Information Content in Organic Molecules: Aggregation States and Solvent Effects.
1223-1236
Electronic Edition (link) BibTeX
- Tharun Kumar Allu, Tudor I. Oprea:
Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry.
1237-1243
Electronic Edition (link) BibTeX
- Mats G. Gustafsson:
Independent Component Analysis Yields Chemically Interpretable Latent Variables in Multivariate Regression.
1244-1255
Electronic Edition (link) BibTeX
- Ester Papa, Fulvio Villa, Paola Gramatica:
Statistically Validated QSARs, Based on Theoretical Descriptors, for Modeling Aquatic Toxicity of Organic Chemicals in Pimephales promelas (Fathead Minnow).
1256-1266
Electronic Edition (link) BibTeX
Computational Chemistry
- Matheus Froeyen, Piet Herdewijn:
Correct Bond Order Assignment in a Molecular Framework Using Integer Linear Programming with Application to Molecules Where Only Non-Hydrogen Atom Coordinates Are Available.
1267-1274
Electronic Edition (link) BibTeX
- Ludovic Kurunczi, Edward Seclaman, Tudor I. Oprea, Luminita Crisan, Zeno Simon:
MTD-PLS: A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor.
1275-1281
Electronic Edition (link) BibTeX
- Anna Vulpetti, Patrizia Crivori, Alexander Cameron, Jay Bertrand, Maria Gabriella Brasca, Roberto D'Alessio, Paolo Pevarello:
Structure-Based Approaches to Improve Selectivity: CDK2-GSK3beta Binding Site Analysis.
1282-1290
Electronic Edition (link) BibTeX
- Iris Antes, Christian Merkwirth, Thomas Lengauer:
POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions.
1291-1302
Electronic Edition (link) BibTeX
- Duangkamol Tantanak, Jumras Limtrakul, Matthew Paul Gleeson:
Probing the Structural and Electronic Factors Affecting the Adsorption and Reactivity of Alkenes in Acidic Zeolites Using DFT Calculations and Multivariate Statistical Methods.
1303-1312
Electronic Edition (link) BibTeX
- Marie M. Ahlström, Marianne Ridderström, Kristina Luthman, Ismael Zamora:
Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields.
1313-1323
Electronic Edition (link) BibTeX
Computational Biochemistry
- Nicole A. Kratochwil, Pari Malherbe, Lothar Lindemann, Martin Ebeling, Marius C. Hoener, Andreas Mühlemann, Richard H. P. Porter, Martin Stahl, Paul R. Gerber:
An Automated System for the Analysis of G Protein-Coupled Receptor Transmembrane Binding Pockets: Alignment, Receptor-Based Pharmacophores, and Their Application.
1324-1336
Electronic Edition (link) BibTeX
Pharmaceutical Modeling
- Ron Jones, Paul C. Connolly, Andreas Klamt, Michael Diedenhofen:
Use of Surface Charges from DFT Calculations To Predict Intestinal Absorption.
1337-1342
Electronic Edition (link) BibTeX
- Hsin-Yuan Wei, Keng-Chang Tsai, Thy-Hou Lin:
Modeling Ligand-Receptor Interaction for Some MHC Class II HLA-DR4 Peptide Mimetic Inhibitors Using Several Molecular Docking and 3D QSAR Techniques.
1343-1351
Electronic Edition (link) BibTeX
- Kunal Roy, J. Thomas Leonard:
QSAR Analyses of 3-(4-Benzylpiperidin-1-yl)-N-phenylpropylamine Derivatives as Potent CCR5 Antagonists.
1352-1368
Electronic Edition (link) BibTeX
- Andreas Bender, Robert C. Glen:
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication.
1369-1375
Electronic Edition (link) BibTeX
- Hu Li, Chun Wei Yap, Choong Yong Ung, Ying Xue, Zhi Wei Cao, Yu Zong Chen:
Effect of Selection of Molecular Descriptors on the Prediction of Blood-Brain Barrier Penetrating and Nonpenetrating Agents by Statistical Learning Methods.
1376-1384
Electronic Edition (link) BibTeX
- Brian W. Clare, Claudiu T. Supuran:
Predictive Flip Regression: A Technique for QSAR of Derivatives of Symmetric Molecules.
1385-1391
Electronic Edition (link) BibTeX
Bioinformatics
Software Description
- Ralph T. Mosley, J. Christopher Culberson, Bryan Kraker, Bradley P. Feuston, Robert P. Sheridan, John F. Conway, Joseph K. Forbes, Subhas J. Chakravorty, Simon K. Kearsley:
Reagent Selector: Using Synthon Analysis to Visualize Reagent Properties and Assist in Combinatorial Library Design.
1439-1446
Electronic Edition (link) BibTeX
- Rafal Gieleciak, Tomasz Magdziarz, Andrzej Bak, Jaroslaw Polanski:
Modeling Robust QSAR. 1. Coding Molecules in 3D-QSAR - from a Point to Surface Sectors and Molecular Volumes.
1447-1455
Electronic Edition (link) BibTeX
- Frank Oellien, Wolf-Dietrich Ihlenfeldt, Johann Gasteiger:
InfVis - Platform-Independent Visual Data Mining of Multidimensional Chemical Data Sets.
1456-1467
Electronic Edition (link) BibTeX
Computer Software Reviews
Volume 45,
Number 6,
November 2005
Articles Articles
- Federico Marini, Alessandra Roncaglioni, Marjana Novic:
Variable Selection and Interpretation in Structure-Affinity Correlation Modeling of Estrogen Receptor Binders.
1507-1519
Electronic Edition (link) BibTeX
- Katalin Tenger, Petro Khoroshyy, Balázs Leitgeb, Gábor Rákhely, Natalia Borovok, Alexander Kotlyar, Dmitry A. Dolgikh, László Zimányi:
Complex Kinetics of the Electron Transfer between the Photoactive Redox Label TUPS and the Heme of Cytochrome c.
1520-1526
Electronic Edition (link) BibTeX
- Klavdija Kutnar, Aleksander Malnic, Dragan Marusic:
Chirality of Toroidal Molecular Graphs.
1527-1535
Electronic Edition (link) BibTeX
- Pavle R. Andjus, Aleksandar Bajic, Lan Zhu, Piergiorgio Strata:
Metabotropic Glutamate Receptor-Mediated Currents at the Climbing Fiber to Purkinje Cell Synapse.
1536-1538
Electronic Edition (link) BibTeX
- Mauro Dalla Serra, Manuela Coraiola, Gabriella Viero, Massimiliano Comai, Cristina Potrich, Mercedes Ferreras, Lamine Baba-Moussa, Didier A. Colin, Gianfranco Menestrina, Sucharit Bhakdi, Gilles Prévost:
Staphylococcus aureus Bicomponent gamma-Hemolysins, HlgA, HlgB, and HlgC, Can Form Mixed Pores Containing All Components.
1539-1545
Electronic Edition (link) BibTeX
- Urban Bren, Milan Hodoscek, Joze Koller:
Development and Validation of Empirical Force Field Parameters for Netropsin.
1546-1552
Electronic Edition (link) BibTeX
- Magdy Lucic Lavcevic, Pavo Dubcek, Zorica Crnjak Orel, Aleksandra Turkovic:
GISAXS View of Vanadium/Cerium Oxide Thin Films and Influence of Lithium Intercalation.
1553-1557
Electronic Edition (link) BibTeX
- Marjan Sterk, Roman Trobec:
Biomedical Simulation of Heat Transfer in a Human Heart.
1558-1563
Electronic Edition (link) BibTeX
- Philippe Huetz, Nasim Mavaddat, Janez Mavri:
Reaction between Ellagic Acid and an Ultimate Carcinogen.
1564-1570
Electronic Edition (link) BibTeX
- Matej Praprotnik, Dusanka Janezic:
Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations.
1571-1579
Electronic Edition (link) BibTeX
- Marilena Di Valentin, Arianna Bisol, Giancarlo Agostini, Donatella Carbonera:
Electronic Coupling Effects on Photoinduced Electron Transfer in Carotene-Porphyrin-Fullerene Triads Detected by Time-Resolved EPR.
1580-1588
Electronic Edition (link) BibTeX
- David Halozan, Christophe Déjugnat, Milan Brumen, Gleb B. Sukhorukov:
Entrapment of a Weak Polyanion and H+/Na+ Exchange in Confined Polyelectrolyte Microcapsules.
1589-1592
Electronic Edition (link) BibTeX
- Franci Merzel, Jeremy C. Smith:
High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data.
1593-1599
Electronic Edition (link) BibTeX
- Urban Borstnik, Dusanka Janezic:
Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers.
1600-1604
Electronic Edition (link) BibTeX
- Ales Fajmut, Marko Jagodic, Milan Brumen:
Mathematical Modeling of the Myosin Light Chain Kinase Activation.
1605-1609
Electronic Edition (link) BibTeX
- Ales Fajmut, Andrej Dobovisek, Milan Brumen:
Mathematical Modeling of the Relation between Myosin Phosphorylation and Stress Development in Smooth Muscles.
1610-1615
Electronic Edition (link) BibTeX
- Dubravka Krilov, Janko N. Herak:
Probabilistic Kinetic Model of Slow Oxidation of Low-Density Lipoprotein. 3. Hydroperoxide-Free Initiation.
1616-1620
Electronic Edition (link) BibTeX
- David Stopar, Janez Strancar, Ruud B. Spruijt, Marcus A. Hemminga:
Exploring the Local Conformational Space of a Membrane Protein by Site-Directed Spin Labeling.
1621-1627
Electronic Edition (link) BibTeX
- Aleh A. Kavalenka, Bogdan Filipic, Marcus A. Hemminga, Janez Strancar:
Speeding Up a Genetic Algorithm for EPR-Based Spin Label Characterization of Biosystem Complexity.
1628-1635
Electronic Edition (link) BibTeX
- Marija Raguz, Jasminka Brnjas-Kraljevic:
Resolved Fluorescence Emission Spectra of PRODAN in Ethanol/Buffer Solvents.
1636-1640
Electronic Edition (link) BibTeX
- Árpád Karsai, Attila Nagy, András Kengyel, Zsolt Mártonfalvi, László Grama, Botondtól Penke, Miklós S. Z. Kellermayer:
Effect of Lysine-28 Side-Chain Acetylation on the Nanomechanical Behavior of Alzheimer Amyloid beta25-35 Fibrils.
1641-1646
Electronic Edition (link) BibTeX
- Igor Weber:
Receptor Occupancy on an Ellipsoidal Cell in the Presence of a Point Source of a Chemoattractant.
1647-1651
Electronic Edition (link) BibTeX
- Miha Fosnaric, Klemen Bohinc, Dorit R. Gauger, Ales Iglic, Veronika Kralj-Iglic, Sylvio May:
The Influence of Anisotropic Membrane Inclusions on Curvature Elastic Properties of Lipid Membranes.
1652-1661
Electronic Edition (link) BibTeX
- Zoran Arsov, Janez Strancar:
Determination of Partition Coefficient of Spin Probe between Different Lipid Membrane Phases.
1662-1671
Electronic Edition (link) BibTeX
- Andrej Vilfan:
Influence of Fluctuations in Actin Structure on Myosin V Step Size.
1672-1675
Electronic Edition (link) BibTeX
- Nejc Tomsiè, Blaz Babnik, Darko Lombardo, Blaz Mavcic, Masa Kanduser, Ales Iglic, Veronika Kralj-Iglic:
Shape and Size of Giant Unilamellar Phospholipid Vesicles Containing Cardiolipin.
1676-1679
Electronic Edition (link) BibTeX
- Ivan Spasojevic, Vuk Maksimovic, Joanna Zakrzewska, Goran Bacic:
Effects of 5-Fluorouracil on Erythrocytes in Relation to Its Cardiotoxicity: Membrane Structure and Functioning.
1680-1685
Electronic Edition (link) BibTeX
- Igor Sersa, Gregor Tratar, Ales Blinc:
Blood Clot Dissolution Dynamics Simulation during Thrombolytic Therapy.
1686-1690
Electronic Edition (link) BibTeX
- Anna Segalla, Ildikó Szabó, Paola Costantini, Giorgio Mario Giacometti:
Study of the Effect of Ion Channel Modulators on Photosynthetic Oxygen Evolution.
1691-1700
Electronic Edition (link) BibTeX
- Tilen Koklic, Mateja Pirs, Reiner Zeisig, Zrinka Abramovic, Marjeta Sentjurc:
Membrane Switch Hypothesis. 1. Cell Density Influences Lateral Domain Structure of Tumor Cell Membranes.
1701-1707
Electronic Edition (link) BibTeX
- Petra Kramaric, Zlatko Pavlica, Tilen Koklic, Alenka Nemec, Nevenka Kozuh Erzen, Marjeta Sentjurc:
Membrane Switch Hypothesis. 2. Domain Structure of Phagocytes in Horses with Recurrent Airway Obstruction.
1708-1715
Electronic Edition (link) BibTeX
- Milos Mojovic, Ivan Spasojevic, Goran Bacic:
Detection of Hydrogen Atom Adduct of Spin-Trap DEPMPO. The Relevance for Studies of Biological Systems.
1716-1718
Electronic Edition (link) BibTeX
Perspective
Articles Chemical Information
- Stephanie E. Harris, A. Guy Orpen, Ian J. Bruno, Robin Taylor:
Factors Affecting d-Block Metal-Ligand Bond Lengths: Toward an Automated Library of Molecular Geometry for Metal Complexes.
1727-1748
Electronic Edition (link) BibTeX
- Yun-De Xiao, Aaron Clauset, Rebecca Harris, Ersin Bayram, Peter Santago II, Jeffrey D. Schmitt:
Supervised Self-Organizing Maps in Drug Discovery. 1. Robust Behavior with Overdetermined Data Sets.
1749-1758
Electronic Edition (link) BibTeX
- Alba T. Macias, Md. Younus Mia, Guanjun Xia, Jun Hayashi, Alexander D. MacKerell Jr.:
Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56lck.
1759-1766
Electronic Edition (link) BibTeX
- Paolo Mazzatorta, Martin Smiesko, Elena Lo Piparo, Emilio Benfenati:
QSAR Model for Predicting Pesticide Aquatic Toxicity.
1767-1774
Electronic Edition (link) BibTeX
- Qing-You Zhang, João Aires-de-Sousa:
Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers.
1775-1783
Electronic Edition (link) BibTeX
- S. Frank Yan, Hayk Asatryan, Jing Li, Yingyao Zhou:
Novel Statistical Approach for Primary High-Throughput Screening Hit Selection.
1784-1790
Electronic Edition (link) BibTeX
- Ralph A. Mansson, Jeremy G. Frey, Jonathan W. Essex, Alan H. Welsh:
Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods.
1791-1803
Electronic Edition (link) BibTeX
- Lei Yang, Peng Wang, Yilin Jiang, Jian Chen:
Studying the Explanatory Capacity of Artificial Neural Networks for Understanding Environmental Chemical Quantitative Structure-Activity Relationship Models.
1804-1811
Electronic Edition (link) BibTeX
- Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath:
Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds.
1812-1819
Electronic Edition (link) BibTeX
- Yongliang Yang, Dmitri V. Nesterenko, Ryan P. Trump, Ken Yamaguchi, Paul A. Bartlett, Dale G. Drueckhammer:
Virtual Hydrocarbon and Combinatorial Databases for Use with CAVEAT.
1820-1823
Electronic Edition (link) BibTeX
- Justin Klekota, Erik Brauner, Stuart L. Schreiber:
Identifying Biologically Active Compound Classes Using Phenotypic Screening Data and Sampling Statistics.
1824-1836
Electronic Edition (link) BibTeX
Computational Chemistry
- Tadeusz Marek Krygowski, Joanna E. Zachara, Robert Moszynski:
Theoretical Study of Changes in pi-Electron Delocalization in the Analogues of an ortho-Hydroxy Schiff Base When the Proton Is Replaced with Li+ or BeH+.
1837-1841
Electronic Edition (link) BibTeX
- Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond:
'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand.
1842-1853
Electronic Edition (link) BibTeX
- Kaushal Rege, Asif Ladiwala, Shanghui Hu, Curt M. Breneman, Jonathan S. Dordick, Steven M. Cramer:
Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (QSAR) Models.
1854-1863
Electronic Edition (link) BibTeX
Computational Biochemistry
Pharmaceutical Modeling
- Samuli-Petrus Korhonen, Kari Tuppurainen, Reino Laatikainen, Mikael Peräkylä:
Comparing the Performance of FLUFF-BALL to SEAL-CoMFA with a Large Diverse Estrogen Data Set: From Relevant Superpositions to Solid Predictions.
1874-1883
Electronic Edition (link) BibTeX
- Michael Fernández, Alain Tundidor-Camba, Julio Caballero:
Modeling of Cyclin-Dependent Kinase Inhibition by 1H-Pyrazolo[3, 4-d]Pyrimidine Derivatives Using Artificial Neural Network Ensembles.
1884-1895
Electronic Edition (link) BibTeX
- Nahoum G. Anthony, Guillaume Huchet, Blair F. Johnston, John A. Parkinson, Colin J. Suckling, Roger D. Waigh, Simon P. Mackay:
In Silico Footprinting of Ligands Binding to the Minor Groove of DNA.
1896-1907
Electronic Edition (link) BibTeX
- Andrew J. S. Knox, Mary J. Meegan, Giorgio Carta, David G. Lloyd:
Considerations in Compound Database Preparation-"Hidden" Impact on Virtual Screening Results.
1908-1919
Electronic Edition (link) BibTeX
- Jianfeng Pei, Hao Chen, Zhenming Liu, Xiaofeng Han, Qi Wang, Bin Shen, Jiaju Zhou, Luhua Lai:
Improving the Quality of 3D-QSAR by Using Flexible-Ligand Receptor Models.
1920-1933
Electronic Edition (link) BibTeX
- Madhu Chopra, Anil K. Mishra:
Ligand-Based Molecular Modeling Study on a Chemically Diverse Series of Cholecystokinin-B/Gastrin Receptor Antagonists: Generation of Predictive Model.
1934-1942
Electronic Edition (link) BibTeX
Software Description
Copyright © Sun May 17 00:07:40 2009
by Michael Ley (ley@uni-trier.de)
