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ORCIDJournal 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, Ana C. A. Roque:
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, Svetlana I. Ovchinnikova, Sergey L. Kuznetsov, Andrey M. Kazennov, Aslan Yu. Tsivadze:
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, Jingsong Yang, Jennifer Borthwick, George Burton, Julien Chabanet, Sophie Bertrand, Helen Evans, Robert J. Young, Junya Qu, Hu Li, Josh Cottom, Paris Ward, Hong Zhang, Thau Ho, Donghui Qin, Siegfried Christensen, Martha S. Head:
Structure-guided optimization of small molecule c-Abl activators. 75-87 - Sachin P. Patil, Pedro J. Ballester, Cassidy R. Kerezsi:
Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition. 89-97 - Te-Lun Mai, Chi-Ming Chen:
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, Karisa L. Wymer, Nathan M. Lim, J. Peter Guthrie:
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, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex:
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, Alpeshkumar K. Malde, Alan E. Mark:
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, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks:
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. 245-257 - Libo Li, Ken A. Dill, Christopher J. Fennell:
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. 259-264 - Oliver Beckstein, Anaïs Fourrier, Bogdan I. Iorga:
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, Michael K. Gilson:
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, Shuai Liu, Nathan M. Lim, Karisa L. Wymer, Alexander L. Perryman, Stefano Forli, Nan-Jie Deng, Justin Su, Kim Branson, Arthur J. Olson:
Blind prediction of HIV integrase binding from the SAMPL4 challenge. 327-345 - Thomas S. Peat, Olan Dolezal, Janet Newman, David L. Mobley, John J. Deadman:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge. 347-362 - Arnout R. D. Voet, Ashutosh Kumar, Francois Berenger, Kam Y. J. Zhang:
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. 363-373 - Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde:
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. 375-400 - Jacob I. Monroe, Michael R. Shirts:
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, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson:
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, Bogdan I. Iorga:
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, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
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, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Alexander D. MacKerell Jr.:
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. 491-507 - Mutasem O. Taha, Maha Habash, Mohammad A. Khanfar:
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, Alexandre Varnek, Aslan Yu. Tsivadze:
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, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang:
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, Sobia Ahsan Halim, Zaheer-ul-Haq, Shagufta Naureen, Saima Rasheed, Shahnaz Perveen, Sajjad Ali, Mohammad Iqbal Choudhary:
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, Alexandre Varnek, Dragos Horvath:
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, Liying Zhang, Alexander Sedykh, Eiichiro Ichiishi, Harukuni Tokuda, Kuo-Hsiung Lee, Hao Zhu:
Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers. 631-646 - Vladimir B. Tsvetkov, Alexander V. Serbin:
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, Ali Ahmed, Mohd Shahir Shamsir, Naomie Salim:
Weighted voting-based consensus clustering for chemical structure databases. 675-684 - Sepideh Parvizpour, Jafar Razmara, Aizi Nor Mazila Ramli, Rosli Md. Illias, Mohd Shahir Shamsir:
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, Carlos Alberto Montanari:
Ligand efficiency metrics considered harmful. 699-710 - David L. Mobley, J. Peter Guthrie:
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, Sangeeta Kundu, Dhananjay Bhattacharyya:
Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs. 735-749 - Seneha Santoshi, Pradeep K. Naik:
Molecular insight of isotypes specific β-tubulin interaction of tubulin heterodimer with noscapinoids. 751-763 - Xin Hu, Patricia M. Legler, Noel Southall, David J. Maloney, Anton Simeonov, Ajit Jadhav:
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, G. Krishnamurthy Rajanikant:
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, Jürgen Bajorath:
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, Ryosuke Suzuki, Ryotaro Tsuji, Yutaka Kuroda:
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, Chris Oostenbrink:
Design of a colicin E7 based chimeric zinc-finger nuclease. 841-850 - Pavan Kumar Pingali, Sukanya Halder, Debasish Mukherjee, Sankar Basu, Rahul Banerjee, Devapriya Choudhury, Dhananjay Bhattacharyya:
Analysis of stacking overlap in nucleic acid structures: algorithm and application. 851-867 - Warachai Praditwongwan, Phimonphan Chuankhayan, Somphot Saoin, Tanchanok Wisitponchai, Vannajan Sanghiran Lee, Sawitree Nangola, Saw See Hong, Philippe Minard, Pierre Boulanger, Chun-Jung Chen, Chatchai Tayapiwatana:
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, Minghao Zheng, Xin Yan, Qiong Gu, Johann Gasteiger, Johan Tijhuis, Peter Maas, Jiabo Li, Jun Xu:
ChemStable: a web server for rule-embedded naïve Bayesian learning approach to predict compound stability. 941-950 - Zdenek Kríz, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koca:
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. 951-960 - Charu Suri, Triscia W. Hendrickson, Harish C. Joshi, Pradeep Kumar Naik:
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, Ye Li:
Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management. 975-988 - Jeremy G. Frey, Colin L. Bird:
Scientific and technical data sharing: a trading perspective. 989-996 - Sean Ekins, Alex M. Clark, S. Joshua Swamidass, Nadia K. Litterman, Antony J. Williams:
Bigger data, collaborative tools and the future of predictive drug discovery. 997-1008 - Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley:
The Protein Data Bank archive as an open data resource. 1009-1014 - Ian J. Bruno, Colin R. Groom:
A crystallographic perspective on sharing data and knowledge. 1015-1022 - Antony J. Williams, Valery Tkachenko:
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, Jan Brase:
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, Samuel Ortega-Salazar, Fernando Gonzales-Nilo, Ehmke Pohl, David S. Holmes, Raquel Quatrini:
AFAL: a web service for profiling amino acids surrounding ligands in proteins. 1069-1076 - Ayax Pérez-Gallegos, Mireia Garcia-Viloca, Àngels González-Lafont, José M. Lluch:
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, Javier Ramos, Victor L. Cruz, Javier Martínez-Salazar:
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, Mire Zloh, Slavica Eric:
Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2. 1109-1128 - Rhiannon L. Kamstra, Saedeh Dadgar, John Wigg, Morshed A. Chowdhury, Christopher P. Phenix, Wely B. Floriano:
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, Alan Prem Kumar, Chun Wei Yap:
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, Adam Zalewski, Angelo Vedani:
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, Martiniano Bello, Roberto Cuevas-Hernández, Rosa Virginia García-Rodríguez, José G. Trujillo-Ferrara, Fernando Rafael Ramos-Morales:
Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures. 1217-1232 - Zhengyu Jiang, Li-Li Xu, Meng-Chen Lu, Yang Pan, Hao-Ze Huang, Xiao-Jin Zhang, Hao-Peng Sun, Qidong You:
Investigation of the intermolecular recognition mechanism between the E3 ubiquitin ligase Keap1 and substrate based on multiple substrates analysis. 1233-1245 - Vikash Kumar, Saman Khan, Priyanka Gupta, Namrata Rastogi, Durga Prasad Mishra, Shakil Ahmed, Mohammad Imran Siddiqi:
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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