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ORCIDJournal of Computer-Aided Molecular Design, Volume 21
Volume 21, Numbers 1-3, January 2007
- Terry R. Stouch, Peter Willett:
Editorial. 1-2 - Rajeshwar P. Verma, Corwin Hansch, Cynthia Rachel Selassie:
Comparative QSAR studies on PAMPA/modified PAMPA for high throughput profiling of drug absorption potential with respect to Caco-2 cells and human intestinal absorption. 3-22 - Richard D. Cramer, Bernd Wendt:
Pushing the boundaries of 3D-QSAR. 23-32 - Johann Gasteiger:
Modeling chemical reactions for drug design. 33-52 - Beining Chen, Robert F. Harrison
, George Papadatos, Peter Willett, David J. Wood, Xiao Qing Lewell, Paulette A. Greenidge, Nikolaus Stiefl:
Evaluation of machine-learning methods for ligand-based virtual screening. 53-62 - Ki Hwan Kim:
Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers? 63-86 - Scott Oloff, Ingo Muegge:
kScore: a novel machine learning approach that is not dependent on the data structure of the training set. 87-95 - Shuxing Zhang, Linyi Wei, Ken Bastow, Weifan Zheng, Arnold Brossi, Kuo-Hsiung Lee, Alexander Tropsha:
Antitumor Agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents. 97-112 - Tudor I. Oprea, Tharun Kumar Allu, Dan C. Fara, Ramona F. Rad, Liliana Ostopovici, Cristian Bologa:
Lead-like, drug-like or "Pub-like": how different are they? 113-119 - Kent D. Stewart, Kevin Steffy, Kevin Harris, John E. Harlan, Vincent S. Stoll, Jeffrey R. Huth, Karl A. Walter, Emily Gramling-Evans, Renaldo Mendoza, Jean M. Severin, Paul L. Richardson, Leo W. Barrett, Edmund D. Matayoshi, Kerry M. Swift, Stephen F. Betz, Steve W. Muchmore, Dale J. Kempf, Akhter Molla:
Design and characterization of an engineered gp41 protein from human immunodeficiency virus-1 as a tool for drug discovery. 121-130 - Akash Khandelwal, Stefan Balaz:
Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods. 131-137 - James T. Metz, Jeffrey R. Huth, Philip J. Hajduk:
Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups. 139-144
Volume 21, Number 4, April 2007
- Zhuoyong Zhang, Liying An, Wenxiang Hu, Yuhong Xiang:
3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach. 145-153 - Ravindra G. Kulkarni, Palukuri Srivani, Garlapati Achaiah, G. Narahari Sastry:
Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: a molecular modeling study. 155-166 - Yovani Marrero-Ponce, Mahmud Tareq Hassan Khan, Gerardo M. Casañola-Martín, Arjumand Ather, Mukhlis N. Sultankhodzhaev, Ramón García-Domenech, Francisco Torrens, Richard Rotondo:
Bond-based 2D TOMOCOMD-CARDD approach for drug discovery: aiding decision-making in 'in silico' selection of new lead tyrosinase inhibitors. 167-188 - Claire L. Gavaghan, Catrin Hasselgren Arnby, Niklas Blomberg, Gert Strandlund, Scott Boyer:
Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data. 189-206 - Armida Di Fenza, Giuliano Alagona, Caterina Ghio, Riccardo Leonardi, Alessandro Giolitti, Andrea Madami:
Caco-2 cell permeability modelling: a neural network coupled genetic algorithm approach. 207-221
Volume 21, Number 5, May 2007
- Ingo Schellhammer, Matthias Rarey:
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. 223-238 - Vassilis Atlamazoglou, Trias Thireou, Elias Eliopoulos:
Using a pharmacophore representation concept to elucidate molecular similarity of dopamine antagonists. 239-249 - Georgia Melagraki, Antreas Afantitis, Haralambos Sarimveis, Panayiotis A. Koutentis, John Markopoulos, Olga Igglessi-Markopoulou:
Optimization of biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists using QSAR modeling, classification techniques and virtual screening. 251-267 - Edward O. Cannon, Ata Amini, Andreas Bender, Michael J. E. Sternberg, Stephen H. Muggleton, Robert C. Glen, John B. O. Mitchell:
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. 269-280 - Ajay N. Jain:
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. 281-306
Volume 21, Number 6, June 2007
- Johann Gasteiger:
De novo design and synthetic accessibility. 307-309 - Krisztina Boda, Thomas Seidel, Johann Gasteiger:
Structure and reaction based evaluation of synthetic accessibility. 311-325 - Juri Pärn, Jörg Degen, Matthias Rarey:
Exploring fragment spaces under multiple physicochemical constraints. 327-340 - Richard D. Cramer, Farhad Soltanshahi, Robert J. Jilek, Brian Campbell:
AllChem: generating and searching 1020 synthetically accessible structures. 341-350 - Jonathan M. Goodman, Ingrid M. Socorro:
Computational assessment of synthetic procedures. 351-357
Volume 21, Number 7, July 2007
- Wendy A. Warr:
Tripos Rediscovered - An Interview with Jim Hopkins, CEO of Tripos Discovery Informatics. 359-360 - Anatoly M. Ruvinsky:
Calculations of protein-ligand binding entropy of relative and overall molecular motions. 361-370 - Alan R. Katritzky, Svetoslav H. Slavov, Dimitar A. Dobchev, Mati Karelson:
QSPR modeling of UV absorption intensities. 371-377 - David J. Diller, Doug W. Hobbs:
Understanding hERG inhibition with QSAR models based on a one-dimensional molecular representation. 379-393 - Erik Evensen, Diane Joseph-McCarthy, Gregory A. Weiss, Stuart L. Schreiber, Martin Karplus:
Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. 395-418 - Masha Y. Niv, Lucy Skrabanek, Marta Filizola, Harel Weinstein:
Modeling activated states of GPCRs: the rhodopsin template. 419
Volume 21, Number 8, August 2007
- Ki Hwan Kim:
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers? 421-435 - Birgit Schlegel, Christian Laggner, René Meier, Thierry Langer, David Schnell, Roland Seifert, Holger Stark, Hans-Dieter Höltje, Wolfgang Sippl:
Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening. 437-453 - Luc Roumen, Marijn P. A. Sanders, Koen Pieterse, Peter A. J. Hilbers, Ralf Plate, Erica M. G. Custers, Marcel de Gooyer, Jos F. M. Smits, Ilona P. E. Beugels, Judith M. A. Emmen, Harry C. J. Ottenheijm, Dirk Leysen, J. J. Rob Hermans:
Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics. 455-471 - Jens Lättig, Markus Böhl, Petra Fischer, Sandra Tischer, Claudia Tietböhl, Mario Menschikowski, Herwig O. Gutzeit, Peter Metz, M. Teresa Pisabarro:
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design. 473-483
Volume 21, Number 9, September 2007
- Timon Schroeter, Anton Schwaighofer, Sebastian Mika, Antonius ter Laak, Detlev Sülzle, Ursula Ganzer, Nikolaus Heinrich, Klaus-Robert Müller:
Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules. 485-498 - Andrea Straßer, Hans-Joachim Wittmann:
Analysis of the activation mechanism of the guinea-pig Histamine H1-receptor. 499-509 - Nidhi Singh, Mitchell A. Avery, Christopher R. McCurdy:
Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations. 511-522 - Mieczyslaw Torchala, Marcin Hoffmann:
IA, database of known ligands of aminoacyl-tRNA synthetases. 523-525 - Alan Talevi, Carolina L. Bellera, Eduardo A. Castro, Luis Bruno Blanch:
A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben. 527-538 - Tímea Polgár, Dóra K. Menyhárd, György M. Keserü:
Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets. 539-548
Volume 21, Numbers 10-11, October 2007
- Vsevolod Katritch, Chelsea M. Byrd, Vladimir Tseitin, Dongcheng Dai, Eugene Raush, Maxim Totrov, Ruben Abagyan, Robert Jordan, Dennis E. Hruby:
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. 549-558 - Matthew Paul Gleeson, Andrew M. Davis, Kamaldeep K. Chohan, Stuart Paine, Scott Boyer, Claire L. Gavaghan, Catrin Hasselgren Arnby, Cecilia Kankkonen, Nan Albertson:
Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models. 559-573 - Patrick Markt, Daniela Schuster, Johannes Kirchmair, Christian Laggner, Thierry Langer:
Pharmacophore modeling and parallel screening for PPAR ligands. 575-590 - John H. Van Drie:
Computer-aided drug design: the next 20 years. 591-601 - Manuel Montenegro, Mireia Garcia-Viloca, Àngels González-Lafont, José M. Lluch:
Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate. 603-615 - Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger:
Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios. 617-640 - Qiqing Zhu, Naijie Jing:
Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3. 641-648
Volume 21, Number 12, December 2007
- Daniel R. McMasters:
Guest editorial for special issue on "ADME and Physical Properties". 649-650 - Timon Schroeter, Anton Schwaighofer, Sebastian Mika, Antonius ter Laak, Detlev Sülzle, Ursula Ganzer, Nikolaus Heinrich, Klaus-Robert Müller:
Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules. 651-664 - Pil H. Lee, Lourdes Cucurull-Sanchez, Jing Lu, Yuhua J. Du:
Development of in silico models for human liver microsomal stability. 665-673 - Chakrapani Kalyanaraman, Matthew P. Jacobson:
An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. 675-679 - John C. Shelley, Anuradha Cholleti, Leah L. Frye, Jeremy R. Greenwood, Mathew R. Timlin, Makoto Uchimaya:
Epik: a software program for pK a prediction and protonation state generation for drug-like molecules. 681-691 - Said H. Hilal, Saravanaraj N. Ayyampalayam, Tad S. Whiteside, Lionel A. Carreira:
Calculating physical properties of organic compounds for environmental modeling from molecular structure. 693-708
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