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ORCIDJournal of Computer-Aided Molecular Design, Volume 31
Volume 31, Number 1, January 2017
- Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu
, David L. Mobley, Michael K. Gilson:
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? 1-19 - Matthew R. Sullivan, Punidha Sokkalingam, Thong Nguyen, James P. Donahue, Bruce C. Gibb:
Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands. 21-28 - Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio:
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. 29-44 - Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio:
Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. 45 - Nupur Bansal, Zheng Zheng, David S. Cerutti, Kenneth M. Merz Jr.:
On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. 47-60 - Stefano Bosisio, Antonia S. J. S. Mey, Julien Michel:
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge. 61-70 - Juyong Lee, Florentina Tofoleanu, Frank C. Pickard IV, Gerhard König, Jing Huang, Ana Damjanovic, Minkyung Baek, Chaok Seok, Bernard R. Brooks:
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. 71-85 - Octav Caldararu, Martin A. Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde:
Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). 87-106 - Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard König, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks:
Absolute binding free energies for octa-acids and guests in SAMPL5 - Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. 107-118 - Soumendranath Bhakat, Pär Söderhjelm:
Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics. 119-132 - Jian Yin, Niel M. Henriksen, David R. Slochower, Michael K. Gilson:
The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method. 133-145 - Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong:
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. 147-161
Volume 31, Number 2, February 2017
- Nádia Melo Borges, Peter W. Kenny, Carlos Alberto Montanari, Igor M. Prokopczyk, Jean F. R. Ribeiro, Josmar R. Rocha, Geraldo Rodrigues Sartori:
The influence of hydrogen bonding on partition coefficients. 163-181 - Courtney E. Cox, Jeremy R. Phifer, Larissa Ferreira da Silva, Gabriel Gonçalves Nogueira, Ryan T. Ley, Elizabeth J. O'Loughlin, Ana Karolyne Pereira Barbosa, Brett T. Rygelski, Andrew S. Paluch:
Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection. 183-199 - Kai Liu, Etsurou Watanabe, Hironori Kokubo:
Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. 201-211 - Elena Di Muzio, Daniele Toti, Fabio Polticelli:
DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina. 213-218 - Dhananjay Bhattacharyya, Sukanya Halder, Sankar Basu, Debasish Mukherjee, Prasun Kumar, Manju Bansal:
RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs. 219-235 - Tambi Richa, Soichiro Ide, Ryosuke Suzuki, Teppei Ebina, Yutaka Kuroda:
Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. 237-244
Volume 31, Number 3, March 2017
- Wendy A. Warr:
A CADD-alog of strategies in pharma. 245-247 - Eric S. Manas, Darren V. S. Green:
CADD medicine: design is the potion that can cure my disease. 249-253 - Frank K. Brown, Edward C. Sherer, Scott A. Johnson, M. Katharine Holloway, Bradley Sherborne:
The evolution of drug design at Merck Research Laboratories. 255-266 - Herman van Vlijmen, Renee L. DesJarlais, Tara Mirzadegan:
Computational chemistry at Janssen. 267-273 - Ingo Muegge, Andreas Bergner, Jan M. Kriegl:
Computer-aided drug design at Boehringer Ingelheim. 275-285 - Vickie Tsui, Daniel F. Ortwine, Jeffrey M. Blaney:
Enabling drug discovery project decisions with integrated computational chemistry and informatics. 287-291 - Georgia B. McGaughey, W. Patrick Walters:
Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact. 293-300 - Brock A. Luty, Peter W. Rose:
The need for scientific software engineering in the pharmaceutical industry. 301-304 - Stephen A. St-Gallay, Colin P. Sambrook-Smith:
Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery. 305-308 - Douglas B. Kitchen:
Computer-aided drug discovery research at a global contract research organization. 309-318 - Daria Goldmann, Barbara Zdrazil, Daniela Digles, Gerhard F. Ecker:
Empowering pharmacoinformatics by linked life science data. 319-328 - Terry R. Stouch:
Urgency and austerity as drivers of success. 329-334
Volume 31, Number 4, April 2017
- Mathias M. von Behren, Matthias Rarey:
Ligand-based virtual screening under partial shape constraints. 335-347 - Meagan C. Small, Asaminew H. Aytenfisu, Fang-Yu Lin, Xibing He, Alexander D. MacKerell Jr.:
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. 349-363 - Mohammed Mumtaz Al-Dabbagh, Naomie Salim, Mubarak Himmat, Ali Ahmed, Faisal Saeed:
Quantum probability ranking principle for ligand-based virtual screening. 365-378 - Hisaki Ikebata, Kenta Hongo, Tetsu Isomura, Ryo Maezono, Ryo Yoshida:
Bayesian molecular design with a chemical language model. 379-391 - Jie Cai, Chanjuan Li, Zhihong Liu, Jiewen Du, Jiming Ye, Qiong Gu, Jun Xu:
Predicting DPP-IV inhibitors with machine learning approaches. 393-402 - Minh Khoa Nguyen, Léonard Jaillet, Stéphane Redon:
As-Rigid-As-Possible molecular interpolation paths. 403-417
Volume 31, Number 5, May 2017
- Ann E. Cleves, Ajay N. Jain:
ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. 419-439 - Pavel Sidorov, Birgit Viira, Elisabeth Davioud-Charvet, Uko Maran, Gilles Marcou, Dragos Horvath, Alexandre Varnek:
QSAR modeling and chemical space analysis of antimalarial compounds. 441-451 - Sankar Basu, Fredrik Söderquist, Björn Wallner:
Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins. 453-466 - Andrés F. Marmolejo-Valencia, Karina Martínez-Mayorga:
Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist. 467-482 - Juan Du, Lin Liu, Li Zhong Guo, Xiaojun Yao, Jian Ming Yang:
Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways. 483-495 - Francesca Cardamone, Federico Iacovelli, Giovanni Chillemi, Mattia Falconi, Alessandro Desideri:
A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function. 497-505
Volume 31, Number 6, June 2017
- Sankalp Jain, Melanie Grandits, Lars Richter, Gerhard F. Ecker:
Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP. 507-521 - Shek Ling Chan:
MolAlign: an algorithm for aligning multiple small molecules. 523-546 - Arjun K. Mishra, Nidhi Singh, Pragati Agnihotri, Shikha Mishra, Saurabh P. Singh, Bala K. Kolli, Kwang Poo Chang, Amogh A. Sahasrabuddhe, Mohammad Imran Siddiqi, J. Venkatesh Pratap:
Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization. 547-562 - Gülsah Çifci, Viktorya Aviyente, E. Demet Akten, Gerald Monard:
Assessing protein-ligand binding modes with computational tools: the case of PDE4B. 563-575 - Motonori Tsuji:
Antagonist-perturbation mechanism for activation function-2 fixed motifs: active conformation and docking mode of retinoid X receptor antagonists. 577-585 - Iwona Stawoska, A. Dudzik, M. Wasylewski, M. Jemiola-Rzeminska, Andrzej Skoczowski, K. Strzalka, Maciej Szaleniec:
DFT-based prediction of reactivity of short-chain alcohol dehydrogenase. 587-602
Volume 31, Number 7, July 2017
- Dilyana Dimova, Jürgen Bajorath:
Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds? 603-608 - Giseok Yun, Jaehoon Kim, Do-Nyun Kim:
A critical assessment of finite element modeling approach for protein dynamics. 609-624 - Qi Gao, Yijun Wang, Jiaying Hou, Qizheng Yao, Ji Zhang:
Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products. 625-641 - Matías A. Zúñiga, Joel B. Alderete, Gonzalo A. Jaña, Verónica A. Jiménez:
Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis. 643-652 - Minkyung Baek, Woong-Hee Shin, Hwan Won Chung, Chaok Seok:
GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking. 653-666 - Jalal Z. A. Laloo, Nassirah Laloo, Lydia Rhyman, Ponnadurai Ramasami:
ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations. 667-673 - David Fernández, Rafael Ramis, Joaquín Ortega-Castro, Rodrigo Casasnovas, Bartolomé Vilanova, Juan Frau:
New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs. 675-688
Volume 31, Number 8, August 2017
- Xianjin Xu, Chengfei Yan, Xiaoqin Zou:
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015. 689-699 - Igor I. Baskin, Vitaly P. Solov'ev, Alexander A. Bagatur'yants, Alexandre Varnek:
Predictive cartography of metal binders using generative topographic mapping. 701-714 - Wiktoria Jedwabny, Joanna Panecka-Hofman, Edyta Dyguda-Kazimierowicz, Rebecca C. Wade, W. Andrzej Sokalski:
Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. 715-728 - Shibaji Ghosh, Nellore Bhanu Chandar, Kalyanashis Jana, Bishwajit Ganguly:
Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies. 729-742 - Hwangseo Park, Hye Seon Lee, Bonsu Ku, Sang-Rae Lee, Seung Jun Kim:
Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1. 743-753 - Yvonne Westermaier, Sergio Ruiz-Carmona, Isabelle Theret, Françoise Perron-Sierra, Guillaume Poissonnet, Catherine Dacquet, Jean A. Boutin, Pierre Ducrot, Xavier Barril:
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR. 755-775 - Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong:
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. 777
Volume 31, Number 9, September 2017
- Ryo Kunimoto, Jürgen Bajorath:
Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks. 779-788 - Gijs Schaftenaar, Elias Vlieg, Gert Vriend:
Molden 2.0: quantum chemistry meets proteins. 789-800 - Anacleto Silva de Souza, Marcelo T. de Oliveira, Adriano D. Andricopulo:
Development of a pharmacophore for cruzain using oxadiazoles as virtual molecular probes: quantitative structure-activity relationship studies. 801-816 - Nuno Martinho, Liana C. Silva, Helena F. Florindo, Steve Brocchini, Teresa S. Barata, Mire Zloh:
Practical computational toolkits for dendrimers and dendrons structure design. 817-827 - Pavel G. Polishchuk, Timur I. Madzhidov, Timur Gimadiev, Andrey Bodrov, Ramil I. Nugmanov, Alexandre Varnek:
Structure-reactivity modeling using mixture-based representation of chemical reactions. 829-839 - Golfo G. Kordopati, Haralambos Tzoupis, Anastassios N. Troganis, Gerasimos M. Tsivgoulis, Simona Golic Grdadolnik, Carmen Simal, Theodore V. Tselios:
Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics. 841-854 - Han Cao, Marcus C. K. Ng, Siti Azma Jusoh, Hio Kuan Tai, Shirley W. I. Siu:
TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers. 855-865
Volume 31, Number 10, October 2017
- Samuel Genheden:
Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models. 867-876 - Insun Park, Yu Jin Hwang, TaeHun Kim, Ambily Nath Indu Viswanath, Ashwini M. Londhe, Seo Yun Jung, Kyoung Mi Sim, Sun-Joon Min, Ji Eun Lee, Jihye Seong, Yun Kyung Kim, Kyoung Tai No, Hoon Ryu, Ae Nim Pae:
In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level. 877-889 - Sudipta Samanta, Sanchita Mukherjee:
Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding. 891-903 - Farzaneh Sarrami, Li-Juan Yu, Amir Karton:
Computational design of bio-inspired carnosine-based HOBr antioxidants. 905-913 - Pedro A. Sánchez-Murcia, Álvaro Cortés Cabrera, Federico Gago:
Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B. 915-928 - Insun Park, Ashwini M. Londhe, Ji Woong Lim, Beoung-Geon Park, Seo Yun Jung, Jae Yeol Lee, Sang Min Lim, Kyoung Tai No, Jiyoun Lee, Ae Nim Pae:
Discovery of non-peptidic small molecule inhibitors of cyclophilin D as neuroprotective agents in Aβ-induced mitochondrial dysfunction. 929-941 - Maria Kadukova, Sergei Grudinin:
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization. 943-958
Volume 31, Number 11, November 2017
- Miki Akamatsu, Tudor I. Oprea:
Obituary: Toshio Fujita, QSAR pioneer. 959-960 - Shilva Kayastha, Ryo Kunimoto, Dragos Horvath, Alexandre Varnek, Jürgen Bajorath:
From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. 961-977 - Phani Ghanakota, Heather A. Carlson:
Comparing pharmacophore models derived from crystallography and NMR ensembles. 979-993 - Yushu Ge, Marc van der Kamp, Maturos Malaisree, Dan Liu, Yi Liu, Adrian J. Mulholland:
Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations. 995-1007 - Edson R. A. Oliveira, Ricardo B. de Alencastro, Bruno A. C. Horta:
New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. 1009-1019 - Arik Dahan, Milica Markovic, Shahar Keinan, Igor Kurnikov, Aaron Aponick, Ellen M. Zimmermann, Shimon Ben-Shabat:
Computational modeling and in-vitro/in-silico correlation of phospholipid-based prodrugs for targeted drug delivery in inflammatory bowel disease. 1021-1028 - Yu Wang, Yanzhi Guo, Xuemei Pu, Menglong Li:
Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini. 1029-1038
Volume 31, Number 12, December 2017
- Michio Iwaoka, Toshiki Suzuki, Yuya Shoji, Kenichi Dedachi, Taku Shimosato, Toshiya Minezaki, Hironobu Hojo, Hiroyuki Onuki, Hiroshi Hirota:
Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide. 1039-1052 - Lanlan Li, Wei Wei, Wen-Juan Jia, Yongchang Zhu, Yan Zhang, Jiang-Huai Chen, Jiaqi Tian, Huanxiang Liu, Yong-Xing He, Xiaojun Yao:
Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods. 1053-1062 - Josephine Alba, Maria Jose Marcaida, Jesús Prieto, Guillermo Montoya, Rafael Molina, Marco D'Abramo:
Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI. 1063-1072 - Matthew Habgood:
Bioactive focus in conformational ensembles: a pluralistic approach. 1073-1083 - Julian Zaugg, Yosephine Gumulya, Alpeshkumar K. Malde, Mikael Bodén:
Learning epistatic interactions from sequence-activity data to predict enantioselectivity. 1085-1096 - Farideh Badalkhani-Khamseh, Azadeh Ebrahim-Habibi, Nasser L. Hadipour:
Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers. 1097-1111
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