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Volume 57, Number 1, January 2017 Application Notes
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https://dblp.org/rec/journals/jcisd/GoretAP17 G. Goret , B. Aoun , Eric Pellegrini : MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations. 1-5 export record
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journals/jcisd/CapelliMTC17 share record
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https://dblp.org/rec/journals/jcisd/CapelliMTC17 Riccardo Capelli , Filippo Marchetti , Guido Tiana , Giorgio Colombo : SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold. 6-10
Chemical Information
Computational Chemistry
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https://dblp.org/rec/journals/jcisd/MokB17 N. Yi Mok , Nathan Brown : Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information. 27-35 export record
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https://dblp.org/rec/journals/jcisd/ZangMWJACK17 Qingda Zang , Kamel Mansouri , Antony J. Williams , Richard S. Judson , David G. Allen , Warren M. Casey , Nicole C. Kleinstreuer : In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning. 36-49 share record
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https://dblp.org/rec/journals/jcisd/CaoDS17 Fenglei Cao , Joshua D. Deetz , Huai Sun : Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide. 50-59
Computational Biochemistry
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https://dblp.org/rec/journals/jcisd/SimoesCCRF17 Inês C. M. Simões , Inês P. D. Costa , João T. S. Coimbra , Maria João Ramos , Pedro Alexandrino Fernandes : New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces. 60-72 export record
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https://dblp.org/rec/journals/jcisd/ChaskarZR17 Prasad Chaskar , Vincent Zoete , Ute F. Röhrig : On-the-Fly QM/MM Docking with Attracting Cavities. 73-84 export record
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https://dblp.org/rec/journals/jcisd/Peguero-TejadaV17 Alfredo Peguero-Tejada , Arjan van der Vaart : Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs. 85-92
Pharmaceutical Modeling
Errata
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https://dblp.org/rec/journals/jcisd/HedinHM17 Florent Hédin , Krystel El Hage , Markus Meuwly : Correction to A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations. 102-103 Volume 57, Number 2, February 2017 Application Notes
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journals/jcisd/CapuzziKLTMPT17 share record
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https://dblp.org/rec/journals/jcisd/CapuzziKLTMPT17 Stephen J. Capuzzi , Ian Sang-June Kim , Wai In Lam , Thomas E. Thornton , Eugene N. Muratov , Diane Pozefsky , Alexander Tropsha : Chembench: A Publicly Accessible, Integrated Cheminformatics Portal. 105-108 share record
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https://dblp.org/rec/journals/jcisd/GapsysG17 Vytautas Gapsys , Bert L. de Groot : pmx Webserver: A User Friendly Interface for Alchemistry. 109-114 export record
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https://dblp.org/rec/journals/jcisd/McGuireVVVELLRK17 Ross McGuire , Stefan Verhoeven , Márton Vass , Gerrit Vriend , Iwan J. P. de Esch , Scott J. Lusher , Rob Leurs , Lars Ridder , Albert J. Kooistra , Tina Ritschel , Chris de Graaf : 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. 115-121 export record
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https://dblp.org/rec/journals/jcisd/FlachsenbergAR17 Florian Flachsenberg , Niek Andresen , Matthias Rarey : RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. 122-126
Letters
Chemical Information
Computational Chemistry
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https://dblp.org/rec/journals/jcisd/CallegariLPRMRC17 Donatella Callegari , Alessio Lodola , Daniele Pala , Silvia Rivara , Marco Mor , Andrea Rizzi , Anna Maria Capelli : Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8. 159-169 export record
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https://dblp.org/rec/journals/jcisd/Ben-ShalomPBG17 Ido Y. Ben-Shalom , Stefania Pfeiffer-Marek , Karl-Heinz Baringhaus , Holger Gohlke : Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. 170-189 export record
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https://dblp.org/rec/journals/jcisd/AlogheliOSBK17 Hiba Alogheli , Gustav Olanders , Wesley Schaal , Peter Brandt , Anders Karlén : Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide. 190-202 export record
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https://dblp.org/rec/journals/jcisd/MatsuokaKMMYZ17 Masaki Matsuoka , Ashutosh Kumar , Muhammad Muddassar , Akihisa Matsuyama , Minoru Yoshida , Kam Y. J. Zhang : Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum . 203-213 export record
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https://dblp.org/rec/journals/jcisd/ZhangCZX17 Yuwei Zhang , Zexing Cao , John Zenghui Zhang , Fei Xia : Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules. 214-222
Computational Biochemistry
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https://dblp.org/rec/journals/jcisd/MelikianEBBE17 Maxime Melikian , Baptiste Eluard , Gildas Bertho , Véronique Baud , Nathalie Evrard-Todeschi : Model of the Interaction between the NF-κB Inhibitory Protein p100 and the E3 Ubiquitin Ligase β-TrCP based on NMR and Docking Experiments. 223-233 export record
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https://dblp.org/rec/journals/jcisd/PirilloMRB17 Jenny Pirillo , Gloria Mazzone , Nino Russo , Luca Bertini : Photophysical Properties of S, Se and Te-Substituted Deoxyguanosines: Insight into Their Ability To Act as Chemotherapeutic Agents. 234-242 export record
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https://dblp.org/rec/journals/jcisd/GrossHSJ17 Christine Groß , Kay Hamacher , Katja Schmitz , Sven Jager : Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis. 243-255 export record
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https://dblp.org/rec/journals/jcisd/MagalhaesOCSB17 Pedro R. Magalhães , A. Sofia F. Oliveira , Sara R. R. Campos , Cláudio M. Soares , António M. Baptista : Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study. 256-266 share record
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https://dblp.org/rec/journals/jcisd/GaoZZM17 Ya Gao , Chaomin Zhang , John Z. H. Zhang , Ye Mei : Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. 267-274 export record
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https://dblp.org/rec/journals/jcisd/ZgarbovaJLCSO17 Marie Zgarbová , Petr Jurecka , Filip Lankas , Thomas E. Cheatham III , Jirí Sponer , Michal Otyepka : Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. 275-287 export record
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https://dblp.org/rec/journals/jcisd/JiangLCW17 Xukai Jiang , Wen Li , Guanjun Chen , Lushan Wang : Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. 288-297 export record
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https://dblp.org/rec/journals/jcisd/HaenseleMMRWBDS17 Elke Haensele , Nawel Mele , Marija Miljak , Christopher M. Read , David C. Whitley , Lee Banting , Carla Delépée , Jana Sopkova-de Oliveira Santos , Alban Lepailleur , Ronan Bureau , Jonathan W. Essex , Timothy Clark : Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution. 298-310
Pharmaceutical Modeling
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journals/jcisd/WarszyckiRMKSRC17 share record
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https://dblp.org/rec/journals/jcisd/WarszyckiRMKSRC17 Dawid Warszycki , Manuel Rueda , Stefan Mordalski , Kurt Kristiansen , Grzegorz Satala , Krzysztof Rataj , Zdzislaw Chilmonczyk , Ingebrigt Sylte , Ruben Abagyan , Andrzej J. Bojarski : From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. 311-321 export record
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https://dblp.org/rec/journals/jcisd/RanaCSLCWL17 Neha Rana , Jason M. Conley , Monica Soto-Velasquez , Francisco León , Stephen J. Cutler , Val J. Watts , Markus A. Lill : Molecular Modeling Evaluation of the Enantiomers of a Novel Adenylyl Cyclase 2 Inhibitor. 322-334 export record
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https://dblp.org/rec/journals/jcisd/MukherjeeKDBRMG17 Sreya Mukherjee , Aleksandra Karolak , Marjolaine Debant , Paul Buscaglia , Yves Renaudineau , Olivier Mignen , Wayne C. Guida , Wesley H. Brooks : Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release. 335-344 export record
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https://dblp.org/rec/journals/jcisd/SchauperlCFHWPK17 Michael Schauperl , Paul Czodrowski , Julian E. Fuchs , Roland G. Huber , Birgit J. Waldner , Maren Podewitz , Christian Kramer , Klaus R. Liedl : Binding Pose Flip Explained via Enthalpic and Entropic Contributions. 345-354 export record
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https://dblp.org/rec/journals/jcisd/ZhangFHWLZWL17 Chen Zhang , Ling-Jun Feng , Yi-You Huang , Deyan Wu , Zhe Li , Qian Zhou , Yinuo Wu , Hai-Bin Luo : Discovery of Novel Phosphodiesterase-2A Inhibitors by Structure-Based Virtual Screening, Structural Optimization, and Bioassay. 355-364 export record
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https://dblp.org/rec/journals/jcisd/WiederGPBSAL17 Marcus Wieder , Arthur Garon , Ugo Perricone , Stefan Boresch , Thomas Seidel , Anna Maria Almerico , Thierry Langer : Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations. 365-385
Errata
Volume 57, Number 3, March 2017 Editorial
Application Notes
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Chemical Information
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https://dblp.org/rec/journals/jcisd/CapuzziMT17 Stephen J. Capuzzi , Eugene N. Muratov , Alexander Tropsha : Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. 417-427 share record
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https://dblp.org/rec/journals/jcisd/WagnerH17 Arne Wagner , Hans-Jörg Himmel : aRMSD : A Comprehensive Tool for Structural Analysis. 428-438 export record
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https://dblp.org/rec/journals/jcisd/SvenssonNB17 Fredrik Svensson , Ulf Norinder , Andreas Bender : Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. 439-444 export record
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https://dblp.org/rec/journals/jcisd/VerrasWGGKRPSCG17 Andreas Verras , Chris L. Waller , Peter Gedeck , Darren V. S. Green , Thierry Kogej , Anandkumar Raichurkar , Manoranjan Panda , Anang A. Shelat , Julie Clark , R. Kiplin Guy , George Papadatos , Jeremy N. Burrows : Shared Consensus Machine Learning Models for Predicting Blood Stage Malaria Inhibition. 445-453 share record
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https://dblp.org/rec/journals/jcisd/PottelM17 Joshua Pottel , Nicolas Moitessier : Customizable Generation of Synthetically Accessible, Local Chemical Subspaces. 454-467 export record
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journals/jcisd/FuMLYLZZZSWB17 share record
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https://dblp.org/rec/journals/jcisd/FuMLYLZZZSWB17 Xianjun Fu , Lewis H. Mervin , Xuebo Li , Huayun Yu , Jiaoyang Li , Siti Zuraidah Mohamad Zobir , Azedine Zoufir , Yang Zhou , Yongmei Song , Zhenguo Wang , Andreas Bender : Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis. 468-483 share record
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https://dblp.org/rec/journals/jcisd/LiuN17 Junfeng Liu , Xia Ning : Multi-Assay-Based Compound Prioritization via Assistance Utilization: A Machine Learning Framework. 484-498
Computational Chemistry
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https://dblp.org/rec/journals/jcisd/ZhangBGRGCYX17 Yuezhou Zhang , Alexandre Borrel , Leo Ghemtio , Leslie Regad , Gustav Boije af Gennäs , Anne-Claude Camproux , Jari Yli-Kauhaluoma , Henri Xhaard : Structural Isosteres of Phosphate Groups in the Protein Data Bank. 499-516 share record
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https://dblp.org/rec/journals/jcisd/NgLY17 Wei Chun Ng , Thong Leng Lim , Tiem Leong Yoon : Investigation of Melting Dynamics of Hafnium Clusters. 517-528 export record
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https://dblp.org/rec/journals/jcisd/FriedrichMKSFRK17 Nils-Ole Friedrich , Agnes Meyder , Christina de Bruyn Kops , Kai Sommer , Florian Flachsenberg , Matthias Rarey , Johannes Kirchmair : High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. 529-539 share record
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https://dblp.org/rec/journals/jcisd/Borosky17 Gabriela L. Borosky : Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases. 540-549
Computational Biochemistry
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https://dblp.org/rec/journals/jcisd/EscalanteAWA17 Diego E. Escalante , Kelly G. Aukema , Lawrence P. Wackett , Alptekin Aksan : Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1, 2-Dioxygenase. 550-561 export record
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https://dblp.org/rec/journals/jcisd/DelortRCRMF17 Bartholomé Delort , Pedro Renault , Landry Charlier , Florent Raussin , Jean Martinez , Nicolas Floquet : Coarse-Grained Prediction of Peptide Binding to G-Protein Coupled Receptors. 562-571 export record
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https://dblp.org/rec/journals/jcisd/MeekrathokKNS17 Piyanat Meekrathok , Predrag Kukic , Jens Erik Nielsen , Wipa Suginta : Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pK a Calculations. 572-583 export record
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https://dblp.org/rec/journals/jcisd/DebroiseSC17 Théau Debroise , Eugene I. Shakhnovich , Nicolas Chéron : A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. 584-593
Pharmaceutical Modeling
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https://dblp.org/rec/journals/jcisd/ShaikhSG17 Naeem Shaikh , Mahesh Sharma , Prabha Garg : Selective Fusion of Heterogeneous Classifiers for Predicting Substrates of Membrane Transporters. 594-607 export record
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https://dblp.org/rec/journals/jcisd/KotsampasakouE17 Eleni Kotsampasakou , Gerhard F. Ecker : Predicting Drug-Induced Cholestasis with the Help of Hepatic Transporters - An in Silico Modeling Approach. 608-615 export record
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https://dblp.org/rec/journals/jcisd/DuLCZLTL17 Hanwen Du , Junhao Li , Yingchun Cai , Hongxiao Zhang , Guixia Liu , Yun Tang , Weihua Li : Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery. 616-626 Volume 57, Number 4, April 2017 Application Notes
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https://dblp.org/rec/journals/jcisd/LiuNAMB17 Tairan Liu , Misagh Naderi , Chris Alvin , Supratik Mukhopadhyay , Michal Brylinski : Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with e MolFrag. 627-631 export record
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https://dblp.org/rec/journals/jcisd/MatsubaraAAYN17 Masaaki Matsubara , Kiyoko F. Aoki-Kinoshita , Nobuyuki P. Aoki , Issaku Yamada , Hisashi Narimatsu : WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. 632-637 export record
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https://dblp.org/rec/journals/jcisd/RudikBDDLFP17 Anastasia V. Rudik , Vladislav M. Bezhentsev , Alexander V. Dmitriev , Dmitry S. Druzhilovskiy , Alexey Lagunin , Dmitry Filimonov , Vladimir Poroikov : MetaTox: Web Application for Predicting Structure and Toxicity of Xenobiotics' Metabolites. 638-642 share record
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https://dblp.org/rec/journals/jcisd/AwalePR17 Mahendra Awale , Daniel Probst , Jean-Louis Reymond : WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. 643-649 export record
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https://dblp.org/rec/journals/jcisd/GrahamEK17 James A. Graham , Jonathan W. Essex , Syma Khalid : PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. 650-656
Chemical Information
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https://dblp.org/rec/journals/jcisd/KimJA17 Sungjin Kim , Adrian Jinich , Alán Aspuru-Guzik : MultiDK: A Multiple Descriptor Multiple Kernel Approach for Molecular Discovery and Its Application to Organic Flow Battery Electrolytes. 657-668 export record
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https://dblp.org/rec/journals/jcisd/HuangSWZWJSHXHL17 Shenzhen Huang , Chunli Song , Xiang Wang , Guo Zhang , Yanlin Wang , Xiaojuan Jiang , Qizheng Sun , Luyi Huang , Rong Xiang , Yiguo Hu , Linli Li , Sheng-Yong Yang : Discovery of New SIRT2 Inhibitors by Utilizing a Consensus Docking/Scoring Strategy and Structure-Activity Relationship Analysis. 669-679 export record
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journals/jcisd/Kontijevskis17 share record
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https://dblp.org/rec/journals/jcisd/Kontijevskis17 Aleksejs Kontijevskis : Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks. 680-699 export record
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https://dblp.org/rec/journals/jcisd/VisiniAR17 Ricardo Visini , Mahendra Awale , Jean-Louis Reymond : Fragment Database FDB-17. 700-709 export record
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journals/jcisd/Rodriguez-Perez17 share record
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https://dblp.org/rec/journals/jcisd/Rodriguez-Perez17 Raquel Rodríguez-Pérez , Martin Vogt , Jürgen Bajorath : Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds. 710-716
Computational Chemistry
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https://dblp.org/rec/journals/jcisd/RinaldiGAFMC17 Silvia Rinaldi , Alessandro Gori , Celeste Annovazzi , Erica E. Ferrandi , Daniela Monti , Giorgio Colombo : Unraveling Energy and Dynamics Determinants to Interpret Protein Functional Plasticity: The Limonene-1, 2-epoxide-hydrolase Case Study. 717-725 share record
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https://dblp.org/rec/journals/jcisd/Riniker17 Sereina Riniker : Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. 726-741 share record
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https://dblp.org/rec/journals/jcisd/UeharaT17 Shota Uehara , Shigenori Tanaka : Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations. 742-756
Computational Biochemistry
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https://dblp.org/rec/journals/jcisd/MenyhardHJJP17 Dóra K. Menyhárd , Ilona Hudáky , Imre Jákli , György Juhász , András Perczel : Predictable Conformational Diversity in Foldamers of Sugar Amino Acids. 757-768 export record
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https://dblp.org/rec/journals/jcisd/RasoloheryMG17 Inès Rasolohery , Gautier Moroy , Frédéric Guyon : PatchSearch: A Fast Computational Method for Off-Target Detection. 769-777 export record
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journals/jcisd/KhuntaweeKRIWKR17 share record
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https://dblp.org/rec/journals/jcisd/KhuntaweeKRIWKR17 Wasinee Khuntawee , Manaschai Kunaseth , Chompoonut Rungnim , Suradej Intagorn , Peter Wolschann , Nawee Kungwan , Thanyada Rungrotmongkol , Supot Hannongbua : Comparison of Implicit and Explicit Solvation Models for Iota -Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. 778-786 export record
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journals/jcisd/MladenovicPPSR17 share record
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https://dblp.org/rec/journals/jcisd/MladenovicPPSR17 Milan Mladenovic , Alexandros Patsilinakos , Adele Pirolli , Manuela Sabatino , Rino Ragno : Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H -Chromen-2-One Core: Structure-Based and Ligand-Based Derived Three-Dimensional Quantitative Structure-Activity Relationships Predictive Models. 787-814 export record
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journals/jcisd/AgnihotriMMSSP17 share record
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https://dblp.org/rec/journals/jcisd/AgnihotriMMSSP17 Pragati Agnihotri , Arjun K. Mishra , Shikha Mishra , Vijay Kumar Sirohi , Amogh A. Sahasrabuddhe , J. Venkatesh Pratap : Identification of Novel Inhibitors of Leishmania donovani γ-Glutamylcysteine Synthetase Using Structure-Based Virtual Screening, Docking, Molecular Dynamics Simulation, and in Vitro Studies. 815-825 export record
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https://dblp.org/rec/journals/jcisd/Cossio-PerezPP17 Rodrigo Cossio-Pérez , Juliana Palma , Gustavo Pierdominici-Sottile : Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. 826-834 share record
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https://dblp.org/rec/journals/jcisd/BaiHZLZ17 Zhengya Bai , Shasha Hou , Shilei Zhang , Zhongyan Li , Peng Zhou : Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c -Src. 835-845 export record
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https://dblp.org/rec/journals/jcisd/ArconDMLABTM17 Juan Pablo Arcon , Lucas A. Defelipe , Carlos P. Modenutti , Elias D. López , Daniel Alvarez-Garcia , Xavier Barril , Adrian Gustavo Turjanski , Marcelo A. Marti : Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. 846-863 export record
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https://dblp.org/rec/journals/jcisd/HauserHGSC17 Kevin Hauser , Yiqing He , Miguel Garcia-Diaz , Carlos Simmerling , Evangelos A. Coutsias : Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. 864-874 export record
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https://dblp.org/rec/journals/jcisd/YuanJNLHBLTLTKM17 William Yuan , Dadi Jiang , Dhanya K. Nambiar , Lydia P. Liew , Michael P. Hay , Joshua Bloomstein , Peter Lu , Brandon Turner , Quynh-Thu Le , Robert Tibshirani , Purvesh Khatri , Mark G. Moloney , Albert C. Koong : Chemical Space Mimicry for Drug Discovery. 875-882 export record
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https://dblp.org/rec/journals/jcisd/HarikrishnaP17 S. Harikrishna , P. I. Pradeepkumar : Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. 883-896 export record
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journals/jcisd/WanBSOSBC17 share record
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https://dblp.org/rec/journals/jcisd/WanBSOSBC17 Shunzhou Wan , Agastya Bhati , Sarah Skerratt , Kiyoyuki Omoto , Veerabahu Shanmugasundaram , Sharan K. Bagal , Peter V. Coveney : Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation. 897-909 share record
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https://dblp.org/rec/journals/jcisd/AntalSF17 Zoltan Antal , Janos Szoverfi , Szilard N. Fejer : Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields. 910-917 share record
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https://dblp.org/rec/journals/jcisd/HuMW17 Guodong Hu , Aijing Ma , Jihua Wang : Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations. 918-928
Pharmaceutical Modeling
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journals/jcisd/JafariMACKD17 share record
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https://dblp.org/rec/journals/jcisd/JafariMACKD17 Majid Jafari , Faramarz Mehrnejad , Raheleh Aghdami , Nader Chaparzadeh , Zahra Razaghi Moghadam Kashani , Farahnoosh Doustdar : Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers. 929-941 export record
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journals/jcisd/RagozaHISK17 share record
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https://dblp.org/rec/journals/jcisd/RagozaHISK17 Matthew Ragoza , Joshua Hochuli , Elisa Idrobo , Jocelyn Sunseri , David Ryan Koes : Protein-Ligand Scoring with Convolutional Neural Networks. 942-957 export record
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journals/jcisd/NascimentoOSMA17 share record
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https://dblp.org/rec/journals/jcisd/NascimentoOSMA17 Érica Cristina Moreno Nascimento , Mónica Oliva , Katarzyna Swiderek , João B. L. Martins , Juan Andrés : Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations. 958-976 export record
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journals/jcisd/TianYSWCZWZ17 share record
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https://dblp.org/rec/journals/jcisd/TianYSWCZWZ17 Yuan-xin Tian , Yonghuan Yu , Yudong Shen , Hua Wan , Shan Chang , Tingting Zhang , Shanhe Wan , Jiajie Zhang : Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK. 977-987
Bioinformatics
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https://dblp.org/rec/journals/jcisd/ZhangS17 Yi-Ze Zhang , Hong-Bin Shen : Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features. 988-999 export record
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journals/jcisd/WuLAHCMXFT17 share record
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https://dblp.org/rec/journals/jcisd/WuLAHCMXFT17 Leihong Wu , Zhichao Liu , Scott M. Auerbach , Ruili Huang , Minjun Chen , Kristin McEuen , Joshua Xu , Hong Fang , Weida Tong : Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury. 1000-1006 share record
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https://dblp.org/rec/journals/jcisd/LiY17 Yang Li , Jianyi Yang : Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions. 1007-1012 Volume 57, Number 5, May 2017 Application Notes
Perspectives
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journals/jcisd/BanDLLRC17 share record
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https://dblp.org/rec/journals/jcisd/BanDLLRC17 Fuqiang Ban , Kush Dalal , Huifang Li , Eric Leblanc , Paul S. Rennie , Artem Cherkasov : Best Practices of Computer-Aided Drug Discovery: Lessons Learned from the Development of a Preclinical Candidate for Prostate Cancer with a New Mechanism of Action. 1018-1028
Chemical Information
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journals/jcisd/Gonzalez-Durruthy17 share record
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https://dblp.org/rec/journals/jcisd/Gonzalez-Durruthy17 Michael González-Durruthy , Luciane C. Alberici , Carlos Curti , Zeki Naal , David T. Atique-Sawazaki , José Manuel Vázquez-Naya , Humberto González Díaz , Cristian R. Munteanu : Experimental-Computational Study of Carbon Nanotube Effects on Mitochondrial Respiration: In Silico Nano-QSPR Machine Learning Models Based on New Raman Spectra Transform with Markov-Shannon Entropy Invariants. 1029-1044 export record
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journals/jcisd/TemelsoMKAS17 share record
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https://dblp.org/rec/journals/jcisd/TemelsoMKAS17 Berhane Temelso , Joel M. Mabey , Toshiro Kubota , Nana Appiah-Padi , George C. Shields : ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm. 1045-1054 share record
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https://dblp.org/rec/journals/jcisd/DongXD17 Ying Dong , Bingren Xiang , Ding Du : PVLOO -Based Training Set Selection Improves the External Predictability of QSAR/QSPR Models. 1055-1067
Computational Chemistry
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https://dblp.org/rec/journals/jcisd/HeoLJSL17 Seungryong Heo , Juyong Lee , Keehyoung Joo , Hang-Cheol Shin , Jooyoung Lee : Protein Loop Structure Prediction Using Conformational Space Annealing. 1068-1078 export record
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journals/jcisd/ZhangSPHP17 share record
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https://dblp.org/rec/journals/jcisd/ZhangSPHP17 Tingting Zhang , Gaurav Sharma , Thomas J. Paul , Zachary Hoffmann , Rajeev Prabhakar : Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. 1079-1088 export record
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https://dblp.org/rec/journals/jcisd/WangBLWZL17 Xin Wang , Fu-Quan Bai , Yingtao Liu , Yu Wang , Hong-Xing Zhang , Zhenyang Lin : A Computational Way To Achieve More Effective Candidates for Photodynamic Therapy. 1089-1100
Computational Biochemistry
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journals/jcisd/ChenFWMHYCX17 share record
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https://dblp.org/rec/journals/jcisd/ChenFWMHYCX17 Si Chen , Zhiwei Feng , Yun Wang , Shifan Ma , Ziheng Hu , Peng Yang , Yifeng Chai , Xiang-Qun Xie : Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. 1101-1111 share record
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https://dblp.org/rec/journals/jcisd/YanYJZ17 Yuna Yan , Maoyou Yang , Chang G. Ji , John Z. H. Zhang : Interaction Entropy for Computational Alanine Scanning. 1112-1122 export record
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journals/jcisd/BonomoJO17 share record
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https://dblp.org/rec/journals/jcisd/BonomoJO17 Silvia Bonomo , Flemming Steen Jørgensen , Lars Olsen : Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions. 1123-1133 share record
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https://dblp.org/rec/journals/jcisd/ShaZ17 Hao Sha , Fangqiang Zhu : Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein. 1134-1141 export record
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journals/jcisd/IakovouHL17 share record
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https://dblp.org/rec/journals/jcisd/IakovouHL17 Georgios Iakovou , Steven Hayward ,