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Journal of Computer-Aided Molecular Design, Volume 28
Volume 28, Number 1, January 2014
- Wendy A. Warr:
Data sharing matters. 1-4 - Georgia B. McGaughey, Christopher I. Bayly, Christopher D. Cox, John D. Schreier, Michael J. Breslin, Michael Bogusky, Steve Pitzenberger, Richard Ball, Paul J. Coleman:
Shaping suvorexant: application of experimental and theoretical methods for driving synthetic designs. 5-12 - Li Xing, Brajesh Rai, Elizabeth A. Lunney:
Scaffold mining of kinase hinge binders in crystal structure database. 13-23 - Telma Barroso, Ricardo J. F. Branco
, Ana Aguiar-Ricardo
Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification. 25-34 - Federico Comitani, Netta Cohen, Jamie Ashby, Dominic Botten, Sarah C. R. Lummis, Carla Molteni
Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models. 35-48 - Justin Bo-Kai Hsu, Kai-Yao Huang, Julia Tzu-Ya Weng, Chien-Hsun Huang, Tzong-Yi Lee:
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. 49-60
Volume 28, Number 2, February 2014
- Natalia V. Kireeva
Impact of distance-based metric learning on classification and visualization model performance and structure-activity landscapes. 61-73 - Xuan Hong, Ping Cao, Yoshiaki Washio, Graham Simpson, Nino Campobasso
Structure-guided optimization of small molecule c-Abl activators. 75-87 - Sachin P. Patil, Pedro J. Ballester
Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition. 89-97 - Te-Lun Mai
Computational prediction of kink properties of helices in membrane proteins. 99-109 - Priyanka Thakral, A. K. Bakhshi:
Computational atomistic blueprinting of novel conducting copolymers using particle swarm optimization. 111-122 - Wojciech Kopec, Himanshu Khandelia
Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations. 123-134
Volume 28, Number 3, March 2014
- David L. Mobley
Blind prediction of solvation free energies from the SAMPL4 challenge. 135-150 - J. Peter Guthrie:
SAMPL4, a blind challenge for computational solvation free energies: the compounds considered. 151-168 - Jens Reinisch, Andreas Klamt
Prediction of free energies of hydration with COSMO-RS on the SAMPL4 data set. 169-173 - Hwangseo Park:
Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies. 175-186 - Samuel Genheden
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. 187-200 - Ryan G. Coleman, Teague Sterling, Dahlia R. Weiss:
SAMPL4 & DOCK3.7: lessons for automated docking procedures. 201-209 - Lars Sandberg:
Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge. 211-219 - Katarzyna B. Koziara, Martin Stroet
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. 221-233 - Francesco Manzoni, Pär Söderhjelm
Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field. 235-244 - Gerhard König
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. 245-257 - Libo Li
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. 259-264 - Oliver Beckstein
Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. 265-276 - Hari S. Muddana, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson:
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. 277-287 - Benjamin A. Ellingson, Matthew T. Geballe, Stanislaw Wlodek, Christopher I. Bayly, A. Geoffrey Skillman, Anthony Nicholls:
Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK. 289-298 - Jia Fu, Yu Liu, Jianzhong Wu
Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory. 299-304
Volume 28, Number 4, April 2014
- Hari S. Muddana, Andrew T. Fenley, David L. Mobley
The SAMPL4 host-guest blind prediction challenge: an overview. 305-317 - Corinne L. D. Gibb, Bruce C. Gibb:
Binding of cyclic carboxylates to octa-acid deep-cavity cavitand. 319-325 - David L. Mobley
Blind prediction of HIV integrase binding from the SAMPL4 challenge. 327-345 - Thomas S. Peat
Interrogating HIV integrase for compounds that bind- a SAMPL challenge. 347-362 - Arnout R. D. Voet
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. 363-373 - Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. 375-400 - Jacob I. Monroe
Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. 401-415 - Hervé Hogues, Traian Sulea, Enrico O. Purisima:
Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge. 417-427 - Alexander L. Perryman, Daniel N. Santiago
Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. 429-441 - Ya-Wen Hsiao, Pär Söderhjelm
Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics. 443-454 - Claire Colas
Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset. 455-462 - Hari S. Muddana, Jian Yin, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson:
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. 463-474 - Emilio Gallicchio
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. 475-490
Volume 28, Number 5, May 2014
- Wenbo Yu
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. 491-507 - Mutasem O. Taha
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators. 509-547 - Vitaly P. Solov'ev
QSPR ensemble modelling of the 1: 1 and 1: 2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants. 549-564 - Huei-Tang Wang, Fadlilatul Taufany
Theoretical studies on effective metal-to-ligand charge transfer characteristics of novel ruthenium dyes for dye sensitized solar cells. 565-575 - Khalid M. Khan, Nida Ambreen, Muhammad Taha
Structure-based design, synthesis and biological evaluation of β-glucuronidase inhibitors. 577-585 - Nils Oberhauser, Alessandra Nurisso, Pierre-Alain Carrupt:
MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design. 587-596
Volume 28, Number 6, June 2014
- J. B. Brown, Yasushi Okuno, Gilles Marcou
Computational chemogenomics: Is it more than inductive transfer? 597-618 - Jiesi Luo, Yanzhi Guo, Yun Zhong, Duo Ma, Wenling Li, Menglong Li:
A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity. 619-629 - Brienne Sprague, Qian Shi, Marlene T. Kim
Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers. 631-646 - Vladimir B. Tsvetkov
Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking - Anchors modified polyanions interference with the HIV-1 fusion mediator. 647-673 - Faisal Saeed
Weighted voting-based consensus clustering for chemical structure databases. 675-684 - Sepideh Parvizpour, Jafar Razmara
Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12. 685-698
Volume 28, Number 7, July 2014
- Peter W. Kenny, Andrei Leitão
Ligand efficiency metrics considered harmful. 699-710 - David L. Mobley
FreeSolv: a database of experimental and calculated hydration free energies, with input files. 711-720 - Mohamed Amine Zorgani, Kevin Patron, Mickaël Desvaux
New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface. 721-734 - Sanchita Mukherjee
Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs. 735-749 - Seneha Santoshi
Molecular insight of isotypes specific β-tubulin interaction of tubulin heterodimer with noscapinoids. 751-763 - Xin Hu, Patricia M. Legler, Noel Southall
Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening. 765-778 - S. M. Fayaz
Ensemble pharmacophore meets ensemble docking: a novel screening strategy for the identification of RIPK1 inhibitors. 779-794
Volume 28, Number 8, August 2014
- Gerald M. Maggiora
Chemical space networks: a powerful new paradigm for the description of chemical space. 795-802 - Bernd Wendt, Richard D. Cramer:
Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment. 803-824 - Sreeja Parameswaran, David L. Mobley
Box size effects are negligible for solvation free energies of neutral solutes. 825-829 - Teppei Ebina
H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection. 831-839 - Eszter Németh, Gabriella K. Schilli, Gábor Nagy, Christoph Hasenhindl, Béla Gyurcsik
Design of a colicin E7 based chimeric zinc-finger nuclease. 841-850 - Pavan Kumar Pingali, Sukanya Halder, Debasish Mukherjee, Sankar Basu
Analysis of stacking overlap in nucleic acid structures: algorithm and application. 851-867 - Warachai Praditwongwan, Phimonphan Chuankhayan, Somphot Saoin
Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex. 869-884
Volume 28, Number 9, September 2014
- Anthony Nicholls:
JCAMD special series: statistics and molecular modeling. 885-886 - Anthony Nicholls:
Confidence limits, error bars and method comparison in molecular modeling. Part 1: The calculation of confidence intervals. 887-918 - Bijun Zhang, Martin Vogt, Jürgen Bajorath:
Design of an activity landscape view taking compound-based feature probabilities into account. 919-926 - Angela M. Henzler, Sascha Urbaczek, Matthias Hilbig, Matthias Rarey
An integrated approach to knowledge-driven structure-based virtual screening. 927-939 - Zhihong Liu
ChemStable: a web server for rule-embedded naïve Bayesian learning approach to predict compound stability. 941-950 - Zdenek Kríz, Jan Adam, Jana Mrázková
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. 951-960 - Charu Suri
Molecular insight into γ-γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC). 961-972
Volume 28, Number 10, October 2014
- Wendy A. Warr:
Data sharing as an issue. 973-974 - Leah McEwen
Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management. 975-988 - Jeremy G. Frey
Scientific and technical data sharing: a trading perspective. 989-996 - Sean Ekins, Alex M. Clark, S. Joshua Swamidass
Bigger data, collaborative tools and the future of predictive drug discovery. 997-1008 - Helen M. Berman
The Protein Data Bank archive as an open data resource. 1009-1014 - Ian J. Bruno
A crystallographic perspective on sharing data and knowledge. 1015-1022 - Antony J. Williams
The Royal Society of Chemistry and the delivery of chemistry data repositories for the community. 1023-1030 - Anthony Michael Slater:
The IUPAC aqueous and non-aqueous experimental pKa data repositories of organic acids and bases. 1031-1034 - Janna Neumann
DataCite and DOI names for research data. 1035-1041 - Megan M. Force, Nigel J. Robinson
Encouraging data citation and discovery with the Data Citation Index. 1043-1048
Volume 28, Number 11, November 2014
- Paul Czodrowski
Count on kappa. 1049-1055 - Valère Lounnas, Henry B. Wedler, Timothy Newman, Gijs Schaftenaar, Jason G. Harrison, Gabriella Nepomuceno, Ryan Pemberton, Dean J. Tantillo, Gert Vriend:
Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. 1057-1067 - Mauricio Arenas-Salinas
AFAL: a web service for profiling amino acids surrounding ligands in proteins. 1069-1076 - Ayax Pérez-Gallegos, Mireia Garcia-Viloca
A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant. 1077-1091 - Juan Felipe Franco-Gonzalez
Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. 1093-1107 - Marko Kalinic
Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2. 1109-1128 - Rhiannon L. Kamstra
Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes. 1129-1142 - Veronica M. W. Gee, Fiona S. L. Wong, Lalitha Ramachandran, Gautam Sethi
Identification of novel peroxisome proliferator-activated receptor-gamma (PPARγ) agonists using molecular modeling method. 1143-1151
Volume 28, Number 12, December 2014
- Amrit Sarmah, Ram Kinkar Roy:
A density functional reactivity theory (DFRT) based approach to understand the interaction of cisplatin analogues with protecting agents. 1153-1173 - Soo-Kyung Kim, William A. Goddard III:
Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1. 1175-1190 - Sameh Eid, Noureldin Saleh
Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology. 1191-1204 - Antje Wolf, Sebastian Schoof, Sascha Baumann, Hans-Dieter Arndt, Karl N. Kirschner
Structure-activity relationships of thiostrepton derivatives: implications for rational drug design. 1205-1215 - Margarita Virginia Saavedra-Vélez, José Correa-Basurto, Myrna H. Matus, Eloy Gasca-Pérez
Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures. 1217-1232 - Zhengyu Jiang
Investigation of the intermolecular recognition mechanism between the E3 ubiquitin ligase Keap1 and substrate based on multiple substrates analysis. 1233-1245 - Vikash Kumar
Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents. 1247-1256
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