Journal of Chemical Information and Modeling, Volume 57

Volume 57, Number 1, January 2017

Application Notes

• 
  G. Goret, B. Aoun, E. Pellegrini:
  MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations. 1-5
• 
  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

• 
  Florbela Pereira, Kaixia Xiao, Diogo A. R. S. Latino, Chengcheng Wu, Qing-You Zhang, João Aires-de-Sousa:
  Machine Learning Methods to Predict Density Functional Theory B3LYP Energies of HOMO and LUMO Orbitals. 11-21
• 
  Qian Zhang, Zhijian Xu, Weiliang Zhu:
  The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. 22-26

Computational Chemistry

• 
  N. Yi Mok, Nathan Brown:
  Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information. 27-35
• 
  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
• 
  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

• 
  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
• 
  Prasad Chaskar, Vincent Zoete, Ute F. Röhrig:
  On-the-Fly QM/MM Docking with Attracting Cavities. 73-84
• 
  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

• 
  Nicolas Bosc, Berthold Wroblowski, Christophe Meyer, Pascal Bonnet:
  Prediction of Protein Kinase-Ligand Interactions through 2.5D Kinochemometrics. 93-101

Errata

• 
  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

• 
  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
• 
  Vytautas Gapsys, Bert L. de Groot:
  pmx Webserver: A User Friendly Interface for Alchemistry. 109-114
• 
  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
• 
  Florian Flachsenberg, Niek Andresen, Matthias Rarey:
  RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. 122-126

Letters

• 
  Adam Pecina, Susanta Haldar, Jindrich Fanfrlík, René Meier, Jan Rezác, Martin Lepsík, Pavel Hobza:
  SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses. 127-132

Chemical Information

• 
  Sabina Podlewska, Wojciech M. Czarnecki, Rafal Kafel, Andrzej J. Bojarski:
  Creating the New from the Old: Combinatorial Libraries Generation with Machine-Learning-Based Compound Structure Optimization. 133-147
• 
  Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey:
  Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. 148-158

Computational Chemistry

• 
  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
• 
  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
• 
  Hiba Alogheli, Gustav Olanders, Wesley Schaal, Peter Brandt, Anders Karlén:
  Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide. 190-202
• 
  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
• 
  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

• 
  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
• 
  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
• 
  Christine Groß, Kay Hamacher, Katja Schmitz, Sven Jager:
  Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis. 243-255
• 
  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
• 
  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
• 
  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
• 
  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
• 
  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

• 
  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-HT_1A Receptor Case Study. 311-321
• 
  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
• 
  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
• 
  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
• 
  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
• 
  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

• 
  Donatella Callegari, Alessio Lodola, Daniele Pala, Silvia Rivara, Marco Mor, Andrea Rizzi, Anna Maria Capelli:
  Correction to Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8. 386

Volume 57, Number 3, March 2017

Editorial

• 
  Courtney Aldrich, Carolyn Bertozzi, Gunda I. Georg, Laura Kiessling, Craig Lindsley, Dennis Liotta, Kenneth M. Merz Jr., Alanna Schepartz, Shaomeng Wang:
  The Ecstasy and Agony of Assay Interference Compounds. 387-390

Application Notes

• 
  Federico Zahariev, Nuwan De Silva, Mark S. Gordon, Theresa L. Windus, Marilu Dick-Perez:
  ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data. 391-396
• 
  Mariana González-Medina, Oscar Méndez-Lucio, José L. Medina-Franco:
  Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships. 397-402

Reviews

• 
  Weilin Zhang, Jianfeng Pei, Luhua Lai:
  Computational Multitarget Drug Design. 403-412

Letters

• 
  Malika Kumarasiri, Theodosia Teo, Mingfeng Yu, Stephen Philip, Sunita K. C. Basnet, Hugo Albrecht, Matthew J. Sykes, Peng Wang, Shudong Wang:
  In Search of Novel CDK8 Inhibitors by Virtual Screening. 413-416

Chemical Information

• 
  Stephen J. Capuzzi, Eugene N. Muratov, Alexander Tropsha:
  Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. 417-427
• 
  Arne Wagner, Hans-Jörg Himmel:
  aRMSD: A Comprehensive Tool for Structural Analysis. 428-438
• 
  Fredrik Svensson, Ulf Norinder, Andreas Bender:
  Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. 439-444
• 
  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
• 
  Joshua Pottel, Nicolas Moitessier:
  Customizable Generation of Synthetically Accessible, Local Chemical Subspaces. 454-467
• 
  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
• 
  Junfeng Liu, Xia Ning:
  Multi-Assay-Based Compound Prioritization via Assistance Utilization: A Machine Learning Framework. 484-498

Computational Chemistry

• 
  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
• 
  Wei Chun Ng, Thong Leng Lim, Tiem Leong Yoon:
  Investigation of Melting Dynamics of Hafnium Clusters. 517-528
• 
  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
• 
  Gabriela L. Borosky:
  Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases. 540-549

Computational Biochemistry

• 
  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
• 
  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
• 
  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
• 
  Théau Debroise, Eugene I. Shakhnovich, Nicolas Chéron:
  A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. 584-593

Pharmaceutical Modeling

• 
  Naeem Shaikh, Mahesh Sharma, Prabha Garg:
  Selective Fusion of Heterogeneous Classifiers for Predicting Substrates of Membrane Transporters. 594-607
• 
  Eleni Kotsampasakou, Gerhard F. Ecker:
  Predicting Drug-Induced Cholestasis with the Help of Hepatic Transporters - An in Silico Modeling Approach. 608-615
• 
  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

• 
  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 eMolFrag. 627-631
• 
  Masaaki Matsubara, Kiyoko F. Aoki-Kinoshita, Nobuyuki P. Aoki, Issaku Yamada, Hisashi Narimatsu:
  WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. 632-637
• 
  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
• 
  Mahendra Awale, Daniel Probst, Jean-Louis Reymond:
  WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. 643-649
• 
  James A. Graham, Jonathan W. Essex, Syma Khalid:
  PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. 650-656

Chemical Information

• 
  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
• 
  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
• 
  Aleksejs Kontijevskis:
  Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks. 680-699
• 
  Ricardo Visini, Mahendra Awale, Jean-Louis Reymond:
  Fragment Database FDB-17. 700-709
• 
  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

• 
  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
• 
  Sereina Riniker:
  Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. 726-741
• 
  Shota Uehara, Shigenori Tanaka:
  Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations. 742-756

Computational Biochemistry

• 
  Dóra K. Menyhárd, Ilona Hudáky, Imre Jákli, György Juhász, András Perczel:
  Predictable Conformational Diversity in Foldamers of Sugar Amino Acids. 757-768
• 
  Inès Rasolohery, Gautier Moroy, Frédéric Guyon:
  PatchSearch: A Fast Computational Method for Off-Target Detection. 769-777
• 
  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
• 
  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
• 
  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
• 
  Rodrigo Cossio-Pérez, Juliana Palma, Gustavo Pierdominici-Sottile:
  Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. 826-834
• 
  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
• 
  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
• 
  Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, Evangelos A. Coutsias:
  Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. 864-874
• 
  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
• 
  S. Harikrishna, P. I. Pradeepkumar:
  Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. 883-896
• 
  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
• 
  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
• 
  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

• 
  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
• 
  Matthew Ragoza, Joshua Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes:
  Protein-Ligand Scoring with Convolutional Neural Networks. 942-957
• 
  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
• 
  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

• 
  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
• 
  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
• 
  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

• 
  Rodolpho C. Braga, Vinicius M. Alves, Eugene N. Muratov, Judy Strickland, Nicole C. Kleinstreuer, Alexander Tropsha, Carolina Horta Andrade:
  Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals. 1013-1017

Perspectives

• 
  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

• 
  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
• 
  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
• 
  Ying Dong, Bingren Xiang, Ding Du:
  PV_LOO-Based Training Set Selection Improves the External Predictability of QSAR/QSPR Models. 1055-1067

Computational Chemistry

• 
  Seungryong Heo, Juyong Lee, Keehyoung Joo, Hang-Cheol Shin, Jooyoung Lee:
  Protein Loop Structure Prediction Using Conformational Space Annealing. 1068-1078
• 
  Tingting Zhang, Gaurav Sharma, Thomas J. Paul, Zachary Hoffmann, Rajeev Prabhakar:
  Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. 1079-1088
• 
  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

• 
  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
• 
  Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang:
  Interaction Entropy for Computational Alanine Scanning. 1112-1122
• 
  Silvia Bonomo, Flemming Steen Jørgensen, Lars Olsen:
  Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions. 1123-1133
• 
  Hao Sha, Fangqiang Zhu:
  Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein. 1134-1141
• 
  Georgios Iakovou, Steven Hayward, Stephen D. Laycock:
  Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. 1142-1152
• 
  Wei Ye, Tianle Qian, Hao Liu, Ray Luo, Hai-Feng Chen:
  Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. 1153-1165
• 
  Dong Song, Ray Luo, Hai-Feng Chen:
  The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. 1166-1178
• 
  Jianzhuang Yao, Haixia Luo, Xia Wang:
  Understanding the Catalytic Mechanism and the Substrate Specificity of an Engineered Gluten Hydrolase by QM/MM Molecular Dynamics and Free Energy Simulations. 1179-1186

Pharmaceutical Modeling

• 
  Emanuel S. R. Ehmki, Christian Kramer:
  Matched Molecular Series: Measuring SAR Similarity. 1187-1196
• 
  Malgorzata N. Drwal, Célien Jacquemard, Carlos Perez, Jérémy Desaphy, Esther Kellenberger:
  Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? 1197-1209
•