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@article{DBLP:journals/jcamd/AkamatsuO17,
author = {Miki Akamatsu and
Tudor I. Oprea},
title = {Obituary: Toshio Fujita, {QSAR} pioneer},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {959--960},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0078-6},
doi = {10.1007/S10822-017-0078-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AkamatsuO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Al-DabbaghSHAS17,
author = {Mohammed Mumtaz Al{-}Dabbagh and
Naomie Salim and
Mubarak Himmat and
Ali Ahmed and
Faisal Saeed},
title = {Quantum probability ranking principle for ligand-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {365--378},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0003-4},
doi = {10.1007/S10822-016-0003-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Al-DabbaghSHAS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlbaMPMMD17,
author = {Josephine Alba and
Maria Jose Marcaida and
Jes{\'{u}}s Prieto and
Guillermo Montoya and
Rafael Molina and
Marco D'Abramo},
title = {Structure and dynamics of mesophilic variants from the homing endonuclease
I-DmoI},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1063--1072},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0087-5},
doi = {10.1007/S10822-017-0087-5},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlbaMPMMD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Badalkhani-Khamseh17,
author = {Farideh Badalkhani{-}Khamseh and
Azadeh Ebrahim{-}Habibi and
Nasser L. Hadipour},
title = {Atomistic computer simulations on multi-loaded {PAMAM} dendrimers:
a comparison of amine- and hydroxyl-terminated dendrimers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1097--1111},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0091-9},
doi = {10.1007/S10822-017-0091-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Badalkhani-Khamseh17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaekSCS17,
author = {Minkyung Baek and
Woong{-}Hee Shin and
Hwan Won Chung and
Chaok Seok},
title = {GalaxyDock {BP2} score: a hybrid scoring function for accurate protein-ligand
docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {653--666},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0030-9},
doi = {10.1007/S10822-017-0030-9},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaekSCS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BansalZCM17,
author = {Nupur Bansal and
Zheng Zheng and
David S. Cerutti and
Kenneth M. Merz Jr.},
title = {On the fly estimation of host-guest binding free energies using the
movable type method: participation in the {SAMPL5} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {47--60},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9980-6},
doi = {10.1007/S10822-016-9980-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BansalZCM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaskinSBV17,
author = {Igor I. Baskin and
Vitaly P. Solov'ev and
Alexander A. Bagatur'yants and
Alexandre Varnek},
title = {Predictive cartography of metal binders using generative topographic
mapping},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {701--714},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0033-6},
doi = {10.1007/S10822-017-0033-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaskinSBV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BasuSW17,
author = {Sankar Basu and
Fredrik S{\"{o}}derquist and
Bj{\"{o}}rn Wallner},
title = {Proteus: a random forest classifier to predict disorder-to-order transitioning
binding regions in intrinsically disordered proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {453--466},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0020-y},
doi = {10.1007/S10822-017-0020-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BasuSW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BehrenR17,
author = {Mathias M. von Behren and
Matthias Rarey},
title = {Ligand-based virtual screening under partial shape constraints},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {335--347},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0011-z},
doi = {10.1007/S10822-017-0011-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BehrenR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BhakatS17,
author = {Soumendranath Bhakat and
P{\"{a}}r S{\"{o}}derhjelm},
title = {Resolving the problem of trapped water in binding cavities: prediction
of host-guest binding free energies in the {SAMPL5} challenge by funnel
metadynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {119--132},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9948-6},
doi = {10.1007/S10822-016-9948-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BhakatS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BhattacharyyaHB17,
author = {Dhananjay Bhattacharyya and
Sukanya Halder and
Sankar Basu and
Debasish Mukherjee and
Prasun Kumar and
Manju Bansal},
title = {RNAHelix: computational modeling of nucleic acid structures with Watson-Crick
and non-canonical base pairs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {219--235},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0007-0},
doi = {10.1007/S10822-016-0007-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BhattacharyyaHB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BorgesKMPRRS17,
author = {N{\'{a}}dia Melo Borges and
Peter W. Kenny and
Carlos Alberto Montanari and
Igor M. Prokopczyk and
Jean F. R. Ribeiro and
Josmar R. Rocha and
Geraldo Rodrigues Sartori},
title = {The influence of hydrogen bonding on partition coefficients},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {163--181},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0002-5},
doi = {10.1007/S10822-016-0002-5},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BorgesKMPRRS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BosisioMM17,
author = {Stefano Bosisio and
Antonia S. J. S. Mey and
Julien Michel},
title = {Blinded predictions of host-guest standard free energies of binding
in the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {61--70},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9933-0},
doi = {10.1007/S10822-016-9933-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BosisioMM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrownSJHS17,
author = {Frank K. Brown and
Edward C. Sherer and
Scott A. Johnson and
M. Katharine Holloway and
Bradley Sherborne},
title = {The evolution of drug design at Merck Research Laboratories},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {255--266},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9993-1},
doi = {10.1007/S10822-016-9993-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BrownSJHS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaiLLDYGX17,
author = {Jie Cai and
Chanjuan Li and
Zhihong Liu and
Jiewen Du and
Jiming Ye and
Qiong Gu and
Jun Xu},
title = {Predicting {DPP-IV} inhibitors with machine learning approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {393--402},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0009-6},
doi = {10.1007/S10822-017-0009-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaiLLDYGX17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaldararuORNR17,
author = {Octav Caldararu and
Martin A. Olsson and
Christoph Riplinger and
Frank Neese and
Ulf Ryde},
title = {Binding free energies in the {SAMPL5} octa-acid host-guest challenge
calculated with {DFT-D3} and {CCSD(T)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {87--106},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9957-5},
doi = {10.1007/S10822-016-9957-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaldararuORNR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaoNJTS17,
author = {Han Cao and
Marcus C. K. Ng and
Siti Azma Jusoh and
Hio Kuan Tai and
Shirley W. I. Siu},
title = {{TMDIM:} an improved algorithm for the structure prediction of transmembrane
domains of bitopic dimers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {855--865},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0047-0},
doi = {10.1007/S10822-017-0047-0},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaoNJTS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CardamoneICFD17,
author = {Francesca Cardamone and
Federico Iacovelli and
Giovanni Chillemi and
Mattia Falconi and
Alessandro Desideri},
title = {A molecular dynamics simulation study decodes the early stage of the
disassembly process abolishing the human {SAMHD1} function},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {497--505},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0014-9},
doi = {10.1007/S10822-017-0014-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CardamoneICFD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Chan17,
author = {Shek Ling Chan},
title = {MolAlign: an algorithm for aligning multiple small molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {523--546},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0023-8},
doi = {10.1007/S10822-017-0023-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Chan17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CifciAAM17,
author = {G{\"{u}}lsah {\c{C}}ifci and
Viktorya Aviyente and
E. Demet Akten and
Gerald Monard},
title = {Assessing protein-ligand binding modes with computational tools: the
case of {PDE4B}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {563--575},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0024-7},
doi = {10.1007/S10822-017-0024-7},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CifciAAM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ17,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {ForceGen 3D structure and conformer generation: from small lead-like
molecules to macrocyclic drugs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {419--439},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0015-8},
doi = {10.1007/S10822-017-0015-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CoxPSNLOBRP17,
author = {Courtney E. Cox and
Jeremy R. Phifer and
Larissa Ferreira da Silva and
Gabriel Gon{\c{c}}alves Nogueira and
Ryan T. Ley and
Elizabeth J. O'Loughlin and
Ana Karolyne Pereira Barbosa and
Brett T. Rygelski and
Andrew S. Paluch},
title = {Combining {MOSCED} with molecular simulation free energy calculations
or electronic structure calculations to develop an efficient tool
for solvent formulation and selection},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {183--199},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0001-6},
doi = {10.1007/S10822-016-0001-6},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/CoxPSNLOBRP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DahanMKKAZB17,
author = {Arik Dahan and
Milica Markovic and
Shahar Keinan and
Igor Kurnikov and
Aaron Aponick and
Ellen M. Zimmermann and
Shimon Ben{-}Shabat},
title = {Computational modeling and in-vitro/in-silico correlation of phospholipid-based
prodrugs for targeted drug delivery in inflammatory bowel disease},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1021--1028},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0079-5},
doi = {10.1007/S10822-017-0079-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DahanMKKAZB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DimovaB17,
author = {Dilyana Dimova and
J{\"{u}}rgen Bajorath},
title = {Is scaffold hopping a reliable indicator for the ability of computational
methods to identify structurally diverse active compounds?},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {603--608},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0032-7},
doi = {10.1007/S10822-017-0032-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DimovaB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DuLGYY17,
author = {Juan Du and
Lin Liu and
Li Zhong Guo and
Xiaojun Yao and
Jian Ming Yang},
title = {Molecular basis of {P450} OleTJE: an investigation of substrate binding
mechanism and major pathways},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {483--495},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0013-x},
doi = {10.1007/S10822-017-0013-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DuLGYY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FernandezROCVF17,
author = {David Fern{\'{a}}ndez and
Rafael Ramis and
Joaqu{\'{\i}}n Ortega{-}Castro and
Rodrigo Casasnovas and
Bartolom{\'{e}} Vilanova and
Juan Frau},
title = {New insights into human farnesyl pyrophosphate synthase inhibition
by second-generation bisphosphonate drugs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {675--688},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0034-5},
doi = {10.1007/S10822-017-0034-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FernandezROCVF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaoWHYZ17,
author = {Qi Gao and
Yijun Wang and
Jiaying Hou and
Qizheng Yao and
Ji Zhang},
title = {Multiple receptor-ligand based pharmacophore modeling and molecular
docking to screen the selective inhibitors of matrix metalloproteinase-9
from natural products},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {625--641},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0028-3},
doi = {10.1007/S10822-017-0028-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GaoWHYZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeKMLLM17,
author = {Yushu Ge and
Marc van der Kamp and
Maturos Malaisree and
Dan Liu and
Yi Liu and
Adrian J. Mulholland},
title = {Identification of the quinolinedione inhibitor binding site in Cdc25
phosphatase {B} through docking and molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {995--1007},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0073-y},
doi = {10.1007/S10822-017-0073-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GeKMLLM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Genheden17,
author = {Samuel Genheden},
title = {Solvation free energies and partition coefficients with the coarse-grained
and hybrid all-atom/coarse-grained {MARTINI} models},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {867--876},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0059-9},
doi = {10.1007/S10822-017-0059-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Genheden17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhanakotaC17,
author = {Phani Ghanakota and
Heather A. Carlson},
title = {Comparing pharmacophore models derived from crystallography and {NMR}
ensembles},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {979--993},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0077-7},
doi = {10.1007/S10822-017-0077-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhanakotaC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhoshCJG17,
author = {Shibaji Ghosh and
Nellore Bhanu Chandar and
Kalyanashis Jana and
Bishwajit Ganguly},
title = {Revealing the importance of linkers in K-series oxime reactivators
for tabun-inhibited AChE using quantum chemical, docking and {SMD}
studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {729--742},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0036-3},
doi = {10.1007/S10822-017-0036-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhoshCJG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GoldmannZDE17,
author = {Daria Goldmann and
Barbara Zdrazil and
Daniela Digles and
Gerhard F. Ecker},
title = {Empowering pharmacoinformatics by linked life science data},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {319--328},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9990-4},
doi = {10.1007/S10822-016-9990-4},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GoldmannZDE17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Habgood17,
author = {Matthew Habgood},
title = {Bioactive focus in conformational ensembles: a pluralistic approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1073--1083},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0089-3},
doi = {10.1007/S10822-017-0089-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Habgood17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IkebataHIMY17,
author = {Hisaki Ikebata and
Kenta Hongo and
Tetsu Isomura and
Ryo Maezono and
Ryo Yoshida},
title = {Bayesian molecular design with a chemical language model},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {379--391},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0008-z},
doi = {10.1007/S10822-016-0008-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/IkebataHIMY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IwaokaSSDSMHOH17,
author = {Michio Iwaoka and
Toshiki Suzuki and
Yuya Shoji and
Kenichi Dedachi and
Taku Shimosato and
Toshiya Minezaki and
Hironobu Hojo and
Hiroyuki Onuki and
Hiroshi Hirota},
title = {Development of {SAAP3D} force field and the application to replica-exchange
Monte Carlo simulation for chignolin and C-peptide},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1039--1052},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0084-8},
doi = {10.1007/S10822-017-0084-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IwaokaSSDSMHOH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainGRE17,
author = {Sankalp Jain and
Melanie Grandits and
Lars Richter and
Gerhard F. Ecker},
title = {Structure based classification for bile salt export pump {(BSEP)}
inhibitors using comparative structural modeling of human {BSEP}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {507--521},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0021-x},
doi = {10.1007/S10822-017-0021-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainGRE17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JedwabnyPDWS17,
author = {Wiktoria Jedwabny and
Joanna Panecka{-}Hofman and
Edyta Dyguda{-}Kazimierowicz and
Rebecca C. Wade and
W. Andrzej Sokalski},
title = {Application of a simple quantum chemical approach to ligand fragment
scoring for Trypanosoma brucei pteridine reductase 1 inhibition},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {715--728},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0035-4},
doi = {10.1007/S10822-017-0035-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JedwabnyPDWS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KadukovaG17,
author = {Maria Kadukova and
Sergei Grudinin},
title = {Convex-PL: a novel knowledge-based potential for protein-ligand interactions
deduced from structural databases using convex optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {943--958},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0068-8},
doi = {10.1007/S10822-017-0068-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KadukovaG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KayasthaKHVB17,
author = {Shilva Kayastha and
Ryo Kunimoto and
Dragos Horvath and
Alexandre Varnek and
J{\"{u}}rgen Bajorath},
title = {From bird's eye views to molecular communities: two-layered visualization
of structure-activity relationships in large compound data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {961--977},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0070-1},
doi = {10.1007/S10822-017-0070-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KayasthaKHVB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Kitchen17,
author = {Douglas B. Kitchen},
title = {Computer-aided drug discovery research at a global contract research
organization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {309--318},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9991-3},
doi = {10.1007/S10822-016-9991-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kitchen17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KordopatiTTTGST17,
author = {Golfo G. Kordopati and
Haralambos Tzoupis and
Anastassios N. Troganis and
Gerasimos M. Tsivgoulis and
Simona Golic Grdadolnik and
Carmen Simal and
Theodore V. Tselios},
title = {Biologically relevant conformational features of linear and cyclic
proteolipid protein {(PLP)} peptide analogues obtained by high-resolution
nuclear magnetic resonance and molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {841--854},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0045-2},
doi = {10.1007/S10822-017-0045-2},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KordopatiTTTGST17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KunimotoB17,
author = {Ryo Kunimoto and
J{\"{u}}rgen Bajorath},
title = {Exploring sets of molecules from patents and relationships to other
active compounds in chemical space networks},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {779--788},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0061-2},
doi = {10.1007/S10822-017-0061-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KunimotoB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LalooLRR17,
author = {Jalal Z. A. Laloo and
Nassirah Laloo and
Lydia Rhyman and
Ponnadurai Ramasami},
title = {ExcelAutomat: a tool for systematic processing of files as applied
to quantum chemical calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {667--673},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0031-8},
doi = {10.1007/S10822-017-0031-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LalooLRR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LeeTPKHDBSB17,
author = {Juyong Lee and
Florentina Tofoleanu and
Frank C. Pickard IV and
Gerhard K{\"{o}}nig and
Jing Huang and
Ana Damjanovic and
Minkyung Baek and
Chaok Seok and
Bernard R. Brooks},
title = {Absolute binding free energy calculations of CBClip host-guest systems
in the {SAMPL5} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {71--85},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9968-2},
doi = {10.1007/S10822-016-9968-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LeeTPKHDBSB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiWJZZCTLHY17,
author = {Lanlan Li and
Wei Wei and
Wen{-}Juan Jia and
Yongchang Zhu and
Yan Zhang and
Jiang{-}Huai Chen and
Jiaqi Tian and
Huanxiang Liu and
Yong{-}Xing He and
Xiaojun Yao},
title = {Discovery of small molecules binding to the normal conformation of
prion by combining virtual screening and multiple biological activity
evaluation methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1053--1062},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0086-6},
doi = {10.1007/S10822-017-0086-6},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiWJZZCTLHY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuWK17,
author = {Kai Liu and
Etsurou Watanabe and
Hironori Kokubo},
title = {Exploring the stability of ligand binding modes to proteins by molecular
dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {201--211},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0005-2},
doi = {10.1007/S10822-016-0005-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuWK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LutyR17,
author = {Brock A. Luty and
Peter W. Rose},
title = {The need for scientific software engineering in the pharmaceutical
industry},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {301--304},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9997-x},
doi = {10.1007/S10822-016-9997-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LutyR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ManasG17,
author = {Eric S. Manas and
Darren V. S. Green},
title = {{CADD} medicine: design is the potion that can cure my disease},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {249--253},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0004-3},
doi = {10.1007/S10822-016-0004-3},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ManasG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Marmolejo-Valencia17,
author = {Andr{\'{e}}s F. Marmolejo{-}Valencia and
Karina Mart{\'{\i}}nez{-}Mayorga},
title = {Allosteric modulation model of the mu opioid receptor by herkinorin,
a potent not alkaloidal agonist},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {467--482},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0016-7},
doi = {10.1007/S10822-017-0016-7},
timestamp = {Wed, 17 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Marmolejo-Valencia17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MartinhoSFBBZ17,
author = {Nuno Martinho and
Liana C. Silva and
Helena F. Florindo and
Steve Brocchini and
Teresa S. Barata and
Mire Zloh},
title = {Practical computational toolkits for dendrimers and dendrons structure
design},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {817--827},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0041-6},
doi = {10.1007/S10822-017-0041-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MartinhoSFBBZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McGaugheyW17,
author = {Georgia B. McGaughey and
W. Patrick Walters},
title = {Modeling {\&} Informatics at Vertex Pharmaceuticals Incorporated:
our philosophy for sustained impact},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {293--300},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9994-0},
doi = {10.1007/S10822-016-9994-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/McGaugheyW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MishraSAMSKCSSP17,
author = {Arjun K. Mishra and
Nidhi Singh and
Pragati Agnihotri and
Shikha Mishra and
Saurabh P. Singh and
Bala K. Kolli and
Kwang Poo Chang and
Amogh A. Sahasrabuddhe and
Mohammad Imran Siddiqi and
J. Venkatesh Pratap},
title = {Discovery of novel inhibitors for Leishmania nucleoside diphosphatase
kinase {(NDK)} based on its structural and functional characterization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {547--562},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0022-9},
doi = {10.1007/S10822-017-0022-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MishraSAMSKCSSP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MueggeBK17,
author = {Ingo Muegge and
Andreas Bergner and
Jan M. Kriegl},
title = {Computer-aided drug design at Boehringer Ingelheim},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {275--285},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9975-3},
doi = {10.1007/S10822-016-9975-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MueggeBK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MuzioTP17,
author = {Elena Di Muzio and
Daniele Toti and
Fabio Polticelli},
title = {DockingApp: a user friendly interface for facilitated docking simulations
with AutoDock Vina},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {213--218},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0006-1},
doi = {10.1007/S10822-016-0006-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MuzioTP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenJR17,
author = {Minh Khoa Nguyen and
L{\'{e}}onard Jaillet and
St{\'{e}}phane Redon},
title = {As-Rigid-As-Possible molecular interpolation paths},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {403--417},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0012-y},
doi = {10.1007/S10822-017-0012-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenJR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OliveiraAH17,
author = {Edson R. A. Oliveira and
Ricardo B. de Alencastro and
Bruno A. C. Horta},
title = {New insights into flavivirus biology: the influence of pH over interactions
between prM and {E} proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1009--1019},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0076-8},
doi = {10.1007/S10822-017-0076-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OliveiraAH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PalHKFXLTWKG17,
author = {Rajat Kumar Pal and
Kamran Haider and
Divya Kaur and
William F. Flynn and
Junchao Xia and
Ronald M. Levy and
Tetiana Taran and
Lauren Wickstrom and
Tom Kurtzman and
Emilio Gallicchio},
title = {A combined treatment of hydration and dynamical effects for the modeling
of host-guest binding thermodynamics: the {SAMPL5} blinded challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {29--44},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9956-6},
doi = {10.1007/S10822-016-9956-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PalHKFXLTWKG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PalHKFXLTWKG17a,
author = {Rajat Kumar Pal and
Kamran Haider and
Divya Kaur and
William F. Flynn and
Junchao Xia and
Ronald M. Levy and
Tetiana Taran and
Lauren Wickstrom and
Tom Kurtzman and
Emilio Gallicchio},
title = {Erratum to: {A} combined treatment of hydration and dynamical effects
for the modeling of host-guest binding thermodynamics: the {SAMPL5}
blinded challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {45},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9987-z},
doi = {10.1007/S10822-016-9987-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PalHKFXLTWKG17a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkHKVLJSMLSKN17,
author = {Insun Park and
Yu Jin Hwang and
TaeHun Kim and
Ambily Nath Indu Viswanath and
Ashwini M. Londhe and
Seo Yun Jung and
Kyoung Mi Sim and
Sun{-}Joon Min and
Ji Eun Lee and
Jihye Seong and
Yun Kyung Kim and
Kyoung Tai No and
Hoon Ryu and
Ae Nim Pae},
title = {In silico probing and biological evaluation of SETDB1/ESET-targeted
novel compounds that reduce tri-methylated histone {H3K9} (H3K9me3)
level},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {877--889},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0052-3},
doi = {10.1007/S10822-017-0052-3},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkHKVLJSMLSKN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkLKLK17,
author = {Hwangseo Park and
Hye Seon Lee and
Bonsu Ku and
Sang{-}Rae Lee and
Seung Jun Kim},
title = {Two-track virtual screening approach to identify both competitive
and allosteric inhibitors of human small C-terminal domain phosphatase
1},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {743--753},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0037-2},
doi = {10.1007/S10822-017-0037-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkLKLK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkLLPJLLNLP17,
author = {Insun Park and
Ashwini M. Londhe and
Ji Woong Lim and
Beoung{-}Geon Park and
Seo Yun Jung and
Jae Yeol Lee and
Sang Min Lim and
Kyoung Tai No and
Jiyoun Lee and
Ae Nim Pae},
title = {Discovery of non-peptidic small molecule inhibitors of cyclophilin
{D} as neuroprotective agents in A{\(\beta\)}-induced mitochondrial
dysfunction},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {929--941},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0067-9},
doi = {10.1007/S10822-017-0067-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkLLPJLLNLP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PolishchukMGBNV17,
author = {Pavel G. Polishchuk and
Timur I. Madzhidov and
Timur Gimadiev and
Andrey Bodrov and
Ramil I. Nugmanov and
Alexandre Varnek},
title = {Structure-reactivity modeling using mixture-based representation of
chemical reactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {829--839},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0044-3},
doi = {10.1007/S10822-017-0044-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PolishchukMGBNV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RichaISEK17,
author = {Tambi Richa and
Soichiro Ide and
Ryosuke Suzuki and
Teppei Ebina and
Yutaka Kuroda},
title = {Fast {H-DROP:} {A} thirty times accelerated version of {H-DROP} for
interactive SVM-based prediction of helical domain linkers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {237--244},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9999-8},
doi = {10.1007/S10822-016-9999-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RichaISEK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SamantaM17,
author = {Sudipta Samanta and
Sanchita Mukherjee},
title = {Co-operative intra-protein structural response due to protein-protein
complexation revealed through thermodynamic quantification: study
of MDM2-p53 binding},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {891--903},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0057-y},
doi = {10.1007/S10822-017-0057-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SamantaM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sanchez-MurciaC17,
author = {Pedro A. S{\'{a}}nchez{-}Murcia and
{\'{A}}lvaro Cort{\'{e}}s Cabrera and
Federico Gago},
title = {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}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {915--928},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0066-x},
doi = {10.1007/S10822-017-0066-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sanchez-MurciaC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SarramiYK17,
author = {Farzaneh Sarrami and
Li{-}Juan Yu and
Amir Karton},
title = {Computational design of bio-inspired carnosine-based HOBr antioxidants},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {905--913},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0060-3},
doi = {10.1007/S10822-017-0060-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SarramiYK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchaftenaarVV17,
author = {Gijs Schaftenaar and
Elias Vlieg and
Gert Vriend},
title = {Molden 2.0: quantum chemistry meets proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {789--800},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0042-5},
doi = {10.1007/S10822-017-0042-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchaftenaarVV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShirtsKSYGMCZ17,
author = {Michael R. Shirts and
Christoph Klein and
Jason M. Swails and
Jian Yin and
Michael K. Gilson and
David L. Mobley and
David A. Case and
Ellen D. Zhong},
title = {Lessons learned from comparing molecular dynamics engines on the {SAMPL5}
dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {147--161},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9977-1},
doi = {10.1007/S10822-016-9977-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShirtsKSYGMCZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShirtsKSYGMCZ17a,
author = {Michael R. Shirts and
Christoph Klein and
Jason M. Swails and
Jian Yin and
Michael K. Gilson and
David L. Mobley and
David A. Case and
Ellen D. Zhong},
title = {Erratum to: Lessons learned from comparing molecular dynamics engines
on the {SAMPL5} dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {777},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0043-4},
doi = {10.1007/S10822-017-0043-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShirtsKSYGMCZ17a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SidorovVDMMHV17,
author = {Pavel Sidorov and
Birgit Viira and
Elisabeth Davioud{-}Charvet and
Uko Maran and
Gilles Marcou and
Dragos Horvath and
Alexandre Varnek},
title = {{QSAR} modeling and chemical space analysis of antimalarial compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {441--451},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0019-4},
doi = {10.1007/S10822-017-0019-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SidorovVDMMHV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SmallALHM17,
author = {Meagan C. Small and
Asaminew H. Aytenfisu and
Fang{-}Yu Lin and
Xibing He and
Alexander D. MacKerell Jr.},
title = {Drude polarizable force field for aliphatic ketones and aldehydes,
and their associated acyclic carbohydrates},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {349--363},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0010-0},
doi = {10.1007/S10822-017-0010-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SmallALHM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SouzaOA17,
author = {Anacleto Silva de Souza and
Marcelo T. de Oliveira and
Adriano D. Andricopulo},
title = {Development of a pharmacophore for cruzain using oxadiazoles as virtual
molecular probes: quantitative structure-activity relationship studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {801--816},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0039-0},
doi = {10.1007/S10822-017-0039-0},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SouzaOA17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/St-GallayS17,
author = {Stephen A. St{-}Gallay and
Colin P. Sambrook{-}Smith},
title = {Tools, techniques, organisation and culture of the {CADD} group at
Sygnature Discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {305--308},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9989-x},
doi = {10.1007/S10822-016-9989-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/St-GallayS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StawoskaDWJSSS17,
author = {Iwona Stawoska and
A. Dudzik and
M. Wasylewski and
M. Jemiola{-}Rzeminska and
Andrzej Skoczowski and
K. Strzalka and
Maciej Szaleniec},
title = {DFT-based prediction of reactivity of short-chain alcohol dehydrogenase},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {587--602},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0026-5},
doi = {10.1007/S10822-017-0026-5},
timestamp = {Fri, 06 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/StawoskaDWJSSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Stouch17,
author = {Terry R. Stouch},
title = {Urgency and austerity as drivers of success},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {329--334},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0018-5},
doi = {10.1007/S10822-017-0018-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Stouch17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SullivanSNDG17,
author = {Matthew R. Sullivan and
Punidha Sokkalingam and
Thong Nguyen and
James P. Donahue and
Bruce C. Gibb},
title = {Binding of carboxylate and trimethylammonium salts to octa-acid and
{TEMOA} deep-cavity cavitands},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {21--28},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9925-0},
doi = {10.1007/S10822-016-9925-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SullivanSNDG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TofoleanuLPKHBS17,
author = {Florentina Tofoleanu and
Juyong Lee and
Frank C. Pickard IV and
Gerhard K{\"{o}}nig and
Jing Huang and
Minkyung Baek and
Chaok Seok and
Bernard R. Brooks},
title = {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},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {107--118},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9965-5},
doi = {10.1007/S10822-016-9965-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TofoleanuLPKHBS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TsuiOB17,
author = {Vickie Tsui and
Daniel F. Ortwine and
Jeffrey M. Blaney},
title = {Enabling drug discovery project decisions with integrated computational
chemistry and informatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {287--291},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9988-y},
doi = {10.1007/S10822-016-9988-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TsuiOB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Tsuji17,
author = {Motonori Tsuji},
title = {Antagonist-perturbation mechanism for activation function-2 fixed
motifs: active conformation and docking mode of retinoid {X} receptor
antagonists},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {577--585},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0025-6},
doi = {10.1007/S10822-017-0025-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Tsuji17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VlijmenDM17,
author = {Herman van Vlijmen and
Renee L. DesJarlais and
Tara Mirzadegan},
title = {Computational chemistry at Janssen},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {267--273},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9998-9},
doi = {10.1007/S10822-016-9998-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VlijmenDM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangGPL17,
author = {Yu Wang and
Yanzhi Guo and
Xuemei Pu and
Menglong Li},
title = {Effective prediction of bacterial type {IV} secreted effectors by
combined features of both C-termini and N-termini},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1029--1038},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0080-z},
doi = {10.1007/S10822-017-0080-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangGPL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr17,
author = {Wendy A. Warr},
title = {A CADD-alog of strategies in pharma},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {245--247},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0017-6},
doi = {10.1007/S10822-017-0017-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WestermaierRTPP17,
author = {Yvonne Westermaier and
Sergio Ruiz{-}Carmona and
Isabelle Theret and
Fran{\c{c}}oise Perron{-}Sierra and
Guillaume Poissonnet and
Catherine Dacquet and
Jean A. Boutin and
Pierre Ducrot and
Xavier Barril},
title = {Binding mode prediction and MD/MMPBSA-based free energy ranking for
agonists of REV-ERB{\(\alpha\)}/NCoR},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {755--775},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0040-7},
doi = {10.1007/S10822-017-0040-7},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WestermaierRTPP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XuYZ17,
author = {Xianjin Xu and
Chengfei Yan and
Xiaoqin Zou},
title = {Improving binding mode and binding affinity predictions of docking
by ligand-based search of protein conformations: evaluation in {D3R}
grand challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {689--699},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0038-1},
doi = {10.1007/S10822-017-0038-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XuYZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YinHSG17,
author = {Jian Yin and
Niel M. Henriksen and
David R. Slochower and
Michael K. Gilson},
title = {The {SAMPL5} host-guest challenge: computing binding free energies
and enthalpies from explicit solvent simulations by the attach-pull-release
{(APR)} method},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {133--145},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9970-8},
doi = {10.1007/S10822-016-9970-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YinHSG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YinHSSCMG17,
author = {Jian Yin and
Niel M. Henriksen and
David R. Slochower and
Michael R. Shirts and
Michael Chiu and
David L. Mobley and
Michael K. Gilson},
title = {Overview adcm43.bhtof the {SAMPL5} host-guest challenge: Are we doing
better?},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {1--19},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9974-4},
doi = {10.1007/S10822-016-9974-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YinHSSCMG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YunKK17,
author = {Giseok Yun and
Jaehoon Kim and
Do{-}Nyun Kim},
title = {A critical assessment of finite element modeling approach for protein
dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {609--624},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0027-4},
doi = {10.1007/S10822-017-0027-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YunKK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZauggGMB17,
author = {Julian Zaugg and
Yosephine Gumulya and
Alpeshkumar K. Malde and
Mikael Bod{\'{e}}n},
title = {Learning epistatic interactions from sequence-activity data to predict
enantioselectivity},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1085--1096},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0090-x},
doi = {10.1007/S10822-017-0090-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZauggGMB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZunigaAJJ17,
author = {Mat{\'{\i}}as A. Z{\'{u}}{\~{n}}iga and
Joel B. Alderete and
Gonzalo A. Ja{\~{n}}a and
Ver{\'{o}}nica A. Jim{\'{e}}nez},
title = {Structural insight into the role of Gln293Met mutation on the Peloruside
A/Laulimalide association with {\(\alpha\)}{\(\beta\)}-tubulin from
molecular dynamics simulations, binding free energy calculations and
weak interactions analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {643--652},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0029-2},
doi = {10.1007/S10822-017-0029-2},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZunigaAJJ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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