TY - JOUR AU - Kitchen, D. B. AU - Decornez, H. AU - Furr, J. R. AU - Bajorath, J. PY - 2004 DA - 2004// TI - Docking and scoring in virtual screening for drug discovery: methods and applications JO - Nat Rev Drug Discov VL - 3 UR - https://doi.org/10.1038/nrd1549 DO - 10.1038/nrd1549 ID - Kitchen2004 ER - TY - JOUR AU - Fischer, M. AU - Coleman, R. G. AU - Fraser, J. S. AU - Shoichet, B. K. PY - 2014 DA - 2014// TI - Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery JO - Nat Chem VL - 6 UR - https://doi.org/10.1038/nchem.1954 DO - 10.1038/nchem.1954 ID - Fischer2014 ER - TY - JOUR AU - Hou, X. B. AU - Li, K. S. AU - Yu, X. AU - Sun, J. P. AU - Fang, H. PY - 2015 DA - 2015// TI - Protein flexibility in docking-based virtual screening: discovery of novel lymphoid-specific tyrosine phosphatase inhibitors using multiple crystal structures JO - J Chem Inf Modeling VL - 55 UR - https://doi.org/10.1021/acs.jcim.5b00344 DO - 10.1021/acs.jcim.5b00344 ID - Hou2015 ER - TY - JOUR AU - Pan, A. C. AU - Borhani, D. W. AU - Dror, R. O. AU - Shaw, D. E. PY - 2013 DA - 2013// TI - Molecular determinants of drug–receptor binding kinetics JO - Drug Discov Today VL - 18 UR - https://doi.org/10.1016/j.drudis.2013.02.007 DO - 10.1016/j.drudis.2013.02.007 ID - Pan2013 ER - TY - JOUR AU - Halperin, I. AU - Ma, B. Y. AU - Wolfson, H. AU - Nussinov, R. PY - 2007 DA - 2007// TI - Principles of docking: an overview of search algorithms and a guide to scoring functions JO - Proteins Struct Funct Genet VL - 47 UR - https://doi.org/10.1002/prot.10115 DO - 10.1002/prot.10115 ID - Halperin2007 ER - TY - JOUR AU - Brooijmans, N. AU - Kuntz, I. D. PY - 2003 DA - 2003// TI - Molecular recognition and docking algorithms JO - Annu Rev Biophys Biomol Struct VL - 32 UR - https://doi.org/10.1146/annurev.biophys.32.110601.142532 DO - 10.1146/annurev.biophys.32.110601.142532 ID - Brooijmans2003 ER - TY - JOUR AU - Iorga, B. AU - Herlem, D. AU - Barre, E. AU - Guillou, C. PY - 2006 DA - 2006// TI - Acetylcholine nicotinic receptors: finding the putative binding site of allosteric modulators using the “blind docking” approach JO - J Mol Modeling VL - 12 UR - https://doi.org/10.1007/s00894-005-0057-z DO - 10.1007/s00894-005-0057-z ID - Iorga2006 ER - TY - JOUR AU - Othman, R. AU - Kiat, T. S. AU - Khalid, N. AU - Yusof, R. AU - Newhouse, E. I. AU - Newhouse, J. S. PY - 2008 DA - 2008// TI - Docking of noncompetitive inhibitors into dengue virus type 2 protease: understanding the interactions with allosteric binding sites JO - J Chem Inf Modeling VL - 48 UR - https://doi.org/10.1021/ci700388k DO - 10.1021/ci700388k ID - Othman2008 ER - TY - JOUR AU - Mancera, R. L. PY - 2007 DA - 2007// TI - Molecular modeling of hydration in drug design JO - Curr Opin Drug Discov Dev VL - 10 ID - Mancera2007 ER - TY - JOUR AU - Jeszenoi, N. AU - Bálint, M. AU - Horváth, I. AU - Spoel, D. AU - Hetényi, C. PY - 2016 DA - 2016// TI - Exploration of interfacial hydration networks of target–ligand complexes JO - J Chem Inf Modeling VL - 56 UR - https://doi.org/10.1021/acs.jcim.5b00638 DO - 10.1021/acs.jcim.5b00638 ID - Jeszenoi2016 ER - TY - JOUR AU - Jeszenoi, N. AU - Horvath, I. AU - Balint, M. AU - Spoel, D. AU - Hetenyi, C. PY - 2015 DA - 2015// TI - Mobility-based prediction of hydration structures of protein surfaces JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv093 DO - 10.1093/bioinformatics/btv093 ID - Jeszenoi2015 ER - TY - JOUR AU - Hetenyi, C. AU - Spoel, D. PY - 2011 DA - 2011// TI - Toward prediction of functional protein pockets using blind docking and pocket search algorithms JO - Protein Sci VL - 20 UR - https://doi.org/10.1002/pro.618 DO - 10.1002/pro.618 ID - Hetenyi2011 ER - TY - JOUR AU - Ahmad, M. AU - Helms, V. AU - Lengauer, T. AU - Kalinina, O. V. PY - 2015 DA - 2015// TI - Enthalpy–entropy compensation upon molecular conformational changes JO - J Chem Theory Comput VL - 11 UR - https://doi.org/10.1021/ct501161t DO - 10.1021/ct501161t ID - Ahmad2015 ER - TY - JOUR AU - Ahmad, M. AU - Kalinina, O. AU - Lengauer, T. PY - 2014 DA - 2014// TI - Entropy gain due to water release upon ligand binding JO - J Cheminform VL - 6 UR - https://doi.org/10.1186/1758-2946-6-S1-P35 DO - 10.1186/1758-2946-6-S1-P35 ID - Ahmad2014 ER - TY - JOUR AU - Rastelli, G. AU - Pacchioni, S. AU - Sirawaraporn, W. AU - Sirawaraporn, R. AU - Parenti, M. D. AU - Ferrari, A. M. PY - 2003 DA - 2003// TI - Docking and database screening reveal new classes of plasmodium falciparum dihydrofolate reductase inhibitors JO - J Med Chem VL - 46 UR - https://doi.org/10.1021/jm030781p DO - 10.1021/jm030781p ID - Rastelli2003 ER - TY - JOUR AU - Hetenyi, C. AU - Spoel, D. PY - 2002 DA - 2002// TI - Efficient docking of peptides to proteins without prior knowledge of the binding site JO - Protein Sci VL - 11 UR - https://doi.org/10.1110/ps.0202302 DO - 10.1110/ps.0202302 ID - Hetenyi2002 ER - TY - JOUR AU - Hetenyi, C. AU - Spoel, D. PY - 2006 DA - 2006// TI - Blind docking of drug-sized compounds to proteins with up to a thousand residues JO - FEBS Lett VL - 580 UR - https://doi.org/10.1016/j.febslet.2006.01.074 DO - 10.1016/j.febslet.2006.01.074 ID - Hetenyi2006 ER - TY - JOUR AU - Grinter, S. Z. AU - Zou, X. PY - 2014 DA - 2014// TI - Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design JO - Molecules VL - 19 UR - https://doi.org/10.3390/molecules190710150 DO - 10.3390/molecules190710150 ID - Grinter2014 ER - TY - JOUR AU - Yuriev, E. AU - Holien, J. AU - Ramsland, P. A. PY - 2015 DA - 2015// TI - Improvements, trends, and new ideas in molecular docking: 2012–2013 in review JO - J Mol Recognit VL - 28 UR - https://doi.org/10.1002/jmr.2471 DO - 10.1002/jmr.2471 ID - Yuriev2015 ER - TY - JOUR AU - Yuriev, E. AU - Ramsland, P. A. PY - 2013 DA - 2013// TI - Latest developments in molecular docking: 2010–2011 in review JO - J Mol Recognit VL - 26 UR - https://doi.org/10.1002/jmr.2266 DO - 10.1002/jmr.2266 ID - Yuriev2013 ER - TY - JOUR AU - Hocker, H. J. AU - Rambahal, N. AU - Gorfe, A. A. PY - 2014 DA - 2014// TI - LIBSA—a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles JO - J Chem Inf Model VL - 54 UR - https://doi.org/10.1021/ci400474u DO - 10.1021/ci400474u ID - Hocker2014 ER - TY - JOUR AU - Schindler, C. E. AU - Vries, S. J. AU - Zacharias, M. PY - 2015 DA - 2015// TI - Fully blind peptide-protein docking with pepATTRACT JO - Structure VL - 23 UR - https://doi.org/10.1016/j.str.2015.05.021 DO - 10.1016/j.str.2015.05.021 ID - Schindler2015 ER - TY - JOUR AU - Whalen, K. L. AU - Tussey, K. B. AU - Blanke, S. R. AU - Spies, M. A. PY - 2011 DA - 2011// TI - Nature of allosteric inhibition in glutamate racemase: discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and pK(a) calculations JO - J Phys Chem B. VL - 115 UR - https://doi.org/10.1021/jp201037t DO - 10.1021/jp201037t ID - Whalen2011 ER - TY - JOUR AU - Garcia-Sosa, A. T. AU - Sild, S. AU - Maran, U. PY - 2008 DA - 2008// TI - Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant JO - J Chem Inf Modeling VL - 48 UR - https://doi.org/10.1021/ci800242z DO - 10.1021/ci800242z ID - Garcia-Sosa2008 ER - TY - JOUR AU - Roumenina, L. AU - Bureeva, S. AU - Kantardjiev, A. AU - Karlinsky, D. AU - Andia-Pravdivy, J. E. AU - Sim, R. PY - 2007 DA - 2007// TI - Complement C1q-target proteins recognition is inhibited by electric moment effectors JO - J Mol Recognit VL - 20 UR - https://doi.org/10.1002/jmr.853 DO - 10.1002/jmr.853 ID - Roumenina2007 ER - TY - JOUR AU - Bugatti, A. AU - Giagulli, C. AU - Urbinati, C. AU - Caccuri, F. AU - Chiodelli, P. AU - Oreste, P. PY - 2013 DA - 2013// TI - Molecular interaction studies of HIV-1 matrix protein p17 and heparin: identification of the heparin-binding motif of p17 as a target for the development of multitarget antagonists JO - J Biol Chem VL - 288 UR - https://doi.org/10.1074/jbc.M112.400077 DO - 10.1074/jbc.M112.400077 ID - Bugatti2013 ER - TY - JOUR AU - Kovacs, M. AU - Toth, J. AU - Hetenyi, C. AU - Malnasi-Csizmadia, A. AU - Sellers, J. R. PY - 2004 DA - 2004// TI - Mechanism of blebbistatin inhibition of myosin II JO - J Biol Chem VL - 279 UR - https://doi.org/10.1074/jbc.M405319200 DO - 10.1074/jbc.M405319200 ID - Kovacs2004 ER - TY - JOUR AU - Agarwal, T. AU - Annamalai, N. AU - Khursheed, A. AU - Maiti, T. K. AU - Bin Arsad, H. AU - Siddiqui, M. H. PY - 2015 DA - 2015// TI - Molecular docking and dynamic simulation evaluation of Rohinitib—Cantharidin based novel HSF1 inhibitors for cancer therapy JO - J Mol Graph Modelling VL - 61 UR - https://doi.org/10.1016/j.jmgm.2015.07.003 DO - 10.1016/j.jmgm.2015.07.003 ID - Agarwal2015 ER - TY - JOUR AU - Morris, G. M. AU - Huey, R. AU - Lindstrom, W. AU - Sanner, M. F. AU - Belew, R. K. AU - Goodsell, D. S. PY - 2009 DA - 2009// TI - AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility JO - J Comput Chem VL - 30 UR - https://doi.org/10.1002/jcc.21256 DO - 10.1002/jcc.21256 ID - Morris2009 ER - TY - JOUR AU - Ganesan, A. AU - Coote, M. L. AU - Barakat, K. PY - 2017 DA - 2017// TI - Molecular dynamics-driven drug discovery: leaping forward with confidence JO - Drug Discov Today VL - 22 UR - https://doi.org/10.1016/j.drudis.2016.11.001 DO - 10.1016/j.drudis.2016.11.001 ID - Ganesan2017 ER - TY - JOUR AU - Dror, R. O. AU - Dirks, R. M. AU - Grossman, J. AU - Xu, H. AU - Shaw, D. E. PY - 2012 DA - 2012// TI - Biomolecular simulation: a computational microscope for molecular biology JO - Annu Rev Biophys VL - 41 UR - https://doi.org/10.1146/annurev-biophys-042910-155245 DO - 10.1146/annurev-biophys-042910-155245 ID - Dror2012 ER - TY - JOUR AU - Durrant, J. D. AU - McCammon, J. A. PY - 2011 DA - 2011// TI - Molecular dynamics simulations and drug discovery JO - BMC Biol VL - 9 UR - https://doi.org/10.1186/1741-7007-9-71 DO - 10.1186/1741-7007-9-71 ID - Durrant2011 ER - TY - JOUR AU - Shan, Y. AU - Kim, E. T. AU - Eastwood, M. P. AU - Dror, R. O. AU - Seeliger, M. A. AU - Shaw, D. E. PY - 2011 DA - 2011// TI - How does a drug molecule find its target binding site? JO - J Am Chem Soc VL - 133 UR - https://doi.org/10.1021/ja202726y DO - 10.1021/ja202726y ID - Shan2011 ER - TY - JOUR AU - Buch, I. AU - Giorgino, T. AU - Fabritiis, G. PY - 2011 DA - 2011// TI - Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations JO - Proc Natl Acad Sci USA VL - 108 UR - https://doi.org/10.1073/pnas.1103547108 DO - 10.1073/pnas.1103547108 ID - Buch2011 ER - TY - JOUR AU - Limongelli, V. AU - Bonomi, M. AU - Parrinello, M. PY - 2013 DA - 2013// TI - Funnel metadynamics as accurate binding free-energy method JO - Proc Natl Acad Sci USA VL - 110 UR - https://doi.org/10.1073/pnas.1303186110 DO - 10.1073/pnas.1303186110 ID - Limongelli2013 ER - TY - JOUR AU - Shan, Y. AU - Gnanasambandan, K. AU - Ungureanu, D. AU - Kim, E. T. AU - Hammaren, H. AU - Yamashita, K. PY - 2014 DA - 2014// TI - Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase JO - Nat Struct Mol Biol VL - 21 UR - https://doi.org/10.1038/nsmb.2849 DO - 10.1038/nsmb.2849 ID - Shan2014 ER - TY - JOUR AU - Jensen, M. Ø. AU - Jogini, V. AU - Borhani, D. W. AU - Leffler, A. E. AU - Dror, R. O. AU - Shaw, D. E. PY - 2012 DA - 2012// TI - Mechanism of voltage gating in potassium channels JO - Science VL - 336 UR - https://doi.org/10.1126/science.1216533 DO - 10.1126/science.1216533 ID - Jensen2012 ER - TY - JOUR AU - Borhani, D. W. AU - Shaw, D. E. PY - 2012 DA - 2012// TI - The future of molecular dynamics simulations in drug discovery JO - J Comput Aided Mol Des VL - 26 UR - https://doi.org/10.1007/s10822-011-9517-y DO - 10.1007/s10822-011-9517-y ID - Borhani2012 ER - TY - JOUR AU - Casasnovas, R. AU - Limongelli, V. AU - Tiwary, P. AU - Carloni, P. AU - Parrinello, M. PY - 2017 DA - 2017// TI - Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations JO - J Am Chem Soc VL - 139 UR - https://doi.org/10.1021/jacs.6b12950 DO - 10.1021/jacs.6b12950 ID - Casasnovas2017 ER - TY - JOUR AU - Kuzmanic, A. AU - Sutto, L. AU - Saladino, G. AU - Nebreda, A. R. AU - Gervasio, F. L. AU - Orozco, M. PY - 2017 DA - 2017// TI - Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations JO - eLife VL - 6 UR - https://doi.org/10.7554/eLife.22175 DO - 10.7554/eLife.22175 ID - Kuzmanic2017 ER - TY - JOUR AU - Prakash, P. AU - Hancock, J. F. AU - Gorfe, A. A. PY - 2015 DA - 2015// TI - Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis JO - Proteins Struct Funct Bioinform VL - 83 UR - https://doi.org/10.1002/prot.24786 DO - 10.1002/prot.24786 ID - Prakash2015 ER - TY - JOUR AU - Abraham, M. J. AU - Murtola, T. AU - Schulz, R. AU - Páll, S. AU - Smith, J. C. AU - Hess, B. PY - 2015 DA - 2015// TI - GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers JO - SoftwareX VL - 1 UR - https://doi.org/10.1016/j.softx.2015.06.001 DO - 10.1016/j.softx.2015.06.001 ID - Abraham2015 ER - TY - JOUR AU - Cornell, W. D. AU - Cieplak, P. AU - Bayly, C. I. AU - Gould, I. R. AU - Merz, K. M. AU - Ferguson, D. M. PY - 1995 DA - 1995// TI - A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules JO - J Am Chem Soc VL - 117 UR - https://doi.org/10.1021/ja00124a002 DO - 10.1021/ja00124a002 ID - Cornell1995 ER - TY - JOUR AU - Soderhjelm, P. AU - Tribello, G. A. AU - Parrinello, M. PY - 2012 DA - 2012// TI - Locating binding poses in protein-ligand systems using reconnaissance metadynamics JO - Proc Natl Acad Sci USA VL - 109 UR - https://doi.org/10.1073/pnas.1201940109 DO - 10.1073/pnas.1201940109 ID - Soderhjelm2012 ER - TY - JOUR AU - Dror, R. O. AU - Pan, A. C. AU - Arlow, D. H. AU - Borhani, D. W. AU - Maragakis, P. AU - Shan, Y. B. PY - 2012 DA - 2012// TI - Pathway and mechanism of drug binding to G-protein-coupled receptors JO - Biophys J VL - 102 UR - https://doi.org/10.1016/j.bpj.2011.11.2241 DO - 10.1016/j.bpj.2011.11.2241 ID - Dror2012 ER - TY - JOUR AU - Spoel, D. AU - Maaren, P. J. AU - Larsson, P. AU - Timneanu, N. PY - 2006 DA - 2006// TI - Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media JO - J Phys Chem B VL - 09 UR - https://doi.org/10.1021/jp0572535 DO - 10.1021/jp0572535 ID - Spoel2006 ER - TY - JOUR AU - Schmidtke, P. AU - Luque, F. J. AU - Murray, J. B. AU - Barril, X. PY - 2011 DA - 2011// TI - Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design JO - J Am Chem Soc VL - 133 UR - https://doi.org/10.1021/ja207494u DO - 10.1021/ja207494u ID - Schmidtke2011 ER - TY - JOUR AU - Cohen, P. PY - 2002 DA - 2002// TI - Protein kinases—the major drug targets of the twenty-first century? JO - Nat Rev Drug Discov VL - 1 UR - https://doi.org/10.1038/nrd773 DO - 10.1038/nrd773 ID - Cohen2002 ER - TY - JOUR AU - Shukla, D. AU - Meng, Y. AU - Roux, B. AU - Pande, V. S. PY - 2014 DA - 2014// TI - Activation pathway of Src kinase reveals intermediate states as targets for drug design JO - Nat Commun. VL - 5 UR - https://doi.org/10.1038/ncomms4397 DO - 10.1038/ncomms4397 ID - Shukla2014 ER - TY - JOUR AU - Foda, Z. H. AU - Seeliger, M. A. PY - 2014 DA - 2014// TI - Kinase inhibitors: an allosteric add-on JO - Nat Chem Biol VL - 10 UR - https://doi.org/10.1038/nchembio.1630 DO - 10.1038/nchembio.1630 ID - Foda2014 ER - TY - JOUR AU - Sadowsky, J. D. AU - Burlingame, M. A. AU - Wolan, D. W. AU - McClendon, C. L. AU - Jacobson, M. P. AU - Wells, J. A. PY - 2011 DA - 2011// TI - Turning a protein kinase on or off from a single allosteric site via disulfide trapping JO - Proc Natl Acad Sci USA VL - 108 UR - https://doi.org/10.1073/pnas.1102376108 DO - 10.1073/pnas.1102376108 ID - Sadowsky2011 ER - TY - JOUR AU - Tiwary, P. AU - Limongelli, V. AU - Salvalaglio, M. AU - Parrinello, M. PY - 2015 DA - 2015// TI - Kinetics of protein-ligand unbinding: predicting pathways, rates, and rate-limiting steps JO - Proc Natl Acad Sci USA VL - 112 UR - https://doi.org/10.1073/pnas.1424461112 DO - 10.1073/pnas.1424461112 ID - Tiwary2015 ER -