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Journal of Computer-Aided Molecular Design, Volume 24
Volume 24, Number 1, January 2010
- Abrar Hussain, James L. Melville, Jonathan D. Hirst
:
Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin. 1-15 - Åsmund Rinnan
How the energy evaluation method used in the geometry optimization step affect the quality of the subsequent QSAR/QSPR models. 17-22 - Yongbo Hu, Raymond J. Unwalla, Rajiah Aldrin Denny, Jack Bikker, Li Di, Christine Humblet:
Development of QSAR models for microsomal stability: identification of good and bad structural features for rat, human and mouse microsomal stability. 23-35 - Liang Chang, Changhai Zhou, Man Xu, Jing Liu:
Interactions between anti-ErbB2 antibody A21 and the ErbB2 extracellular domain provide a basis for improving A21 affinity. 37-47 - Eunkyoung Jung, Junhyoung Kim, Seung-Hoon Choi, Minkyoung Kim, Hokyoung Rhee, Jae-Min Shin, Kihang Choi
Artificial neural network study on organ-targeting peptides. 49-56 - Hamed I. Ali
A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors. 57-75 - Mirza Saqib Baig, Ashutosh Kumar, Mohammad Imran Siddiqi, Neena Goyal:
Characterization of dipeptidylcarboxypeptidase of Leishmania donovani: a molecular model for structure based design of antileishmanials. 77-87
Volume 24, Number 2, February 2010
- Yvonne C. Martin, Terry R. Stouch:
Call for papers: Symposium on Tautomers and Biology, American Chemical Society National Meeting, Boston, MA, USA August 2010. 89-90 - Daniel P. Garden, Boris S. Zhorov:
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function. 91-105 - Varnavas D. Mouchlis
Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor. 107-115 - Orazio Nicolotti
Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model. 117-129 - Chin Yee Liew, Xiao Hua Ma, Chun Wei Yap
Consensus model for identification of novel PI3K inhibitors in large chemical library. 131-141 - Prashant Revan Murumkar
Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors. 143-156 - Carolina Horta Andrade
3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents. 157-172
Volume 24, Number 3, March 2010
- A. V. Grigoryan, Irina Kufareva
Spatial chemical distance based on atomic property fields. 173-182 - Alberto Del Rio
A computational workflow for the design of irreversible inhibitors of protein kinases. 183-194 - Vladimir Frecer, Stanislav Miertus
Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease. 195-212 - Soonmin Jang, Tse-Yu Chung, Jungho Shin, Kai-Lun Lin, Jason T. C. Tzen
Docking study of the precursor peptide of matoparan onto its putative processing enzyme, dipeptidyl peptidase IV: a revisit to molecular ticketing. 213-224 - Austin B. Yongye, Marc A. Giulianotti
Conformational landscape of platinum(II)-tetraamine complexes: DFT and NBO studies. 225-235 - Raymond J. Unwalla, Jason B. Cross, Sumeet Salaniwal, Adam D. Shilling, Louis Leung, John Kao, Christine Humblet:
Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism. 237-256
Volume 24, Number 4, April 2010
- A. Geoffrey Skillman, Matthew T. Geballe, Anthony Nicholls:
SAMPL2 challenge: prediction of solvation energies and tautomer ratios. 257-258 - Matthew T. Geballe, A. Geoffrey Skillman, Anthony Nicholls, J. Peter Guthrie, Peter J. Taylor:
The SAMPL2 blind prediction challenge: introduction and overview. 259-279 - Ignacio Soteras
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. 281-291 - Anthony Nicholls, Stanislaw Wlodek, J. Andrew Grant:
SAMPL2 and continuum modeling. 293-306 - Pavel V. Klimovich, David L. Mobley
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. 307-316 - Raphael F. Ribeiro, Aleksandr V. Marenich, Christopher J. Cramer
Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models. 317-333 - Benjamin A. Ellingson, A. Geoffrey Skillman, Anthony Nicholls:
Analysis of SM8 and Zap TK calculations and their geometric sensitivity. 335-342 - Stefan M. Kast, Jochen Heil, Stefan Güssregen, K. Friedemann Schmidt
Prediction of tautomer ratios by embedded-cluster integral equation theory. 343-353 - Stefan M. Kast, Jochen Heil, Stefan Güssregen, K. Friedemann Schmidt:
Erratum to: Prediction of tautomer ratios by embedded-cluster integral equation theory. 355 - Andreas Klamt
Blind prediction test of free energies of hydration with COSMO-RS. 357-360 - Alexandre Meunier, Jean-François Truchon:
Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge. 361-372 - Enrico O. Purisima, Christopher R. Corbeil
Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge. 373-383
Volume 24, Number 5, May 2010
- Jae Yoon Chung
QM/MM based 3D QSAR models for potent B-Raf inhibitors. 385-397 - Ákos Tarcsay, Robert Kiss
Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. 399-408 - Ali Ebrahimi, S. Mostafa Habibi Khorassani
The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs. 409-416 - Daniel Seeliger, Bert L. de Groot:
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. 417-422 - Chaitanya A. K. Koppisetty, Waqas Nasir
Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data. 423-431 - Natasja Brooijmans, Christine Humblet:
Chemical space sampling by different scoring functions and crystal structures. 433-447 - Lourdes Cucurull-Sanchez:
Successful identification of key chemical structure modifications that lead to improved ADME profiles. 449-458 - So-Jung Park, Irina Kufareva
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. 459-471
Volume 24, Numbers 6-7, June 2010
- Yvonne C. Martin:
Overview of the perspectives devoted to tautomerism in molecular design. 473-474 - Alan R. Katritzky, C. Dennis Hall, Bahaa El-Dien M. El-Gendy
Tautomerism in drug discovery. 475-484 - Roger A. Sayle
So you think you understand tautomerism? 485-496 - Wendy A. Warr:
Tautomerism in chemical information management systems. 497-520 - Markus Sitzmann, Wolf-Dietrich Ihlenfeldt, Marc C. Nicklaus
Tautomerism in large databases. 521-551 - William R. Porter:
Warfarin: history, tautomerism and activity. 553-573 - Aurora J. Cruz-Cabeza
Annular tautomerism: experimental observations and quantum mechanics calculations. 575-586 - Rodger F. Henry:
The effects of tautomerism on the nature of molecules in the solid state. 587-590 - Jeremy R. Greenwood, David Calkins, Arron P. Sullivan
Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. 591-604 - Timothy Clark
Tautomers and reference 3D-structures: the orphans of in silico drug design. 605-611 - Yvonne C. Martin:
Tautomerism, Hammett sigma, and QSAR. 613-616 - Richard D. Cramer:
Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling. 617-620 - Andreas Klamt
Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge. 621-625 - Maciej Haranczyk
Combinatorial-computational-chemoinformatics (C3) approach to finding and analyzing low-energy tautomers. 627-638
Volume 24, Number 8, August 2010
- Julien Michel, Jonathan W. Essex:
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. 639-658 - Supriyo Bhattacharya
Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1. 659-674 - Austin B. Yongye, Andreas Bender, Karina Martínez-Mayorga:
Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. 675-686 - Guodong Hu, Dunyou Wang, Xinguo Liu, Qinggang Zhang:
A computational analysis of the binding model of MDM2 with inhibitors. 687-697 - Yuko Okamoto
Dependency of ligand free energy landscapes on charge parameters and solvent models. 699-712 - Eszter Hazai, Istvan Hazai, Laszlo Demko
Cyclodextrin knowledgebase a web-based service managing CD-ligand complexation data. 713-717
Volume 24, Number 9, September 2010
- Jaroslaw J. Panek
Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin - an insight from molecular dynamics simulations with classical and ab initio force fields. 719-732 - Pawel Gruszczynski, Michal Obuchowski
Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis. 733-747 - George Agelis, Panagiota Roumelioti, Amalia Resvani, Serdar Durdagi
An efficient synthesis of a rationally designed 1, 5 disubstituted imidazole AT1 Angiotensin II receptor antagonist: reorientation of imidazole pharmacophore groups in losartan reserves high receptor affinity and confirms docking studies. 749-758 - Andrea Straßer, Hans-Joachim Wittmann:
In silico analysis of the histaprodifen induced activation pathway of the guinea-pig histamine H1-receptor. 759-769 - Giulio Vistoli
Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0. 771-787 - M. Stuart Armstrong, Garrett M. Morris
ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. 789-801
Volume 24, Number 10, October 2010
- Lívia Barros Salum, Napoleão Fonseca Valadares:
Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example. 803-817 - Rizi Ai, M. Qaiser Fatmi, Chia-en A. Chang:
T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles. 819-827 - Faramarz Mehrnejad
Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study. 829-841 - Prabu Manoharan
Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies. 843-864 - Ajay N. Jain:
QMOD: physically meaningful QSAR. 865-878 - Vannajan Sanghiran Lee
Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study. 879-886
Volume 24, Number 11, November 2010
- Wendy A. Warr:
Collaboration, competition, validation and plans for the future - An interview with Gerard Kleywegt, Head of the Protein Data Bank in Europe. 887-890 - Remigijus Didziapetris, Justas Dapkunas
Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition. 891-906 - William F. Long, Paul Labute:
Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors. 907-916 - Tran Trung Tran, Christina Kulis
Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions. 917-934 - Tim ten Brink, Thomas E. Exner
pKa based protonation states and microspecies for protein-ligand docking. 935-942 - Marco Cellanetti, Viswanath Gunda, Li Wang, Antonio Macchiarulo
Insights into the binding mode and mechanism of action of some atypical retinoids as ligands of the small heterodimer partner (SHP). 943-956
Volume 24, Number 12, December 2010
- Matthew D. Segall, Andrew Chadwick:
Making priors a priority. 957-960 - Rafik Karaman:
Prodrugs of aza nucleosides based on proton transfer reaction. 961-970 - Ori Kalid, Martin Mense, Sharon Fischman, Alina Shitrit
Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening. 971-991 - Ping Lan, Mei-Qi Xie, Yue-Mei Yao, Wan-Na Chen, Wei-Min Chen:
3D-QSAR studies and molecular docking on [5-(4-amino-1H-benzoimidazol-2-yl)-furan-2-yl]-phosphonic acid derivatives as fructose-1, 6-biphophatase inhibitors. 993-1008 - Francesco Strino
Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity. 1009-1021 - Marco A. C. Neves, Sérgio Simões
Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach. 1023-1033 - Constanza Cárdenas
Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. 1035-1051 - Natasja Brooijmans, Jason B. Cross, Christine Humblet:
Biased retrieval of chemical series in receptor-based virtual screening. 1053-1062
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