-
1
-
-
84862659868
-
History of Protein-Protein Interactions: From Egg-White to Complex Networks
-
Braun, P.; Gingras, A. C. History of Protein-Protein Interactions: From Egg-White to Complex Networks Proteomics 2012, 12 (10) 1478-1498 10.1002/pmic.201100563
-
(2012)
Proteomics
, vol.12
, Issue.10
, pp. 1478-1498
-
-
Braun, P.1
Gingras, A.C.2
-
2
-
-
84938057090
-
ProPairs: A Data Set for Protein-Protein Docking
-
Krull, F.; Korff, G.; Elghobashi-Meinhardt, N.; Knapp, E. W. ProPairs: A Data Set for Protein-Protein Docking J. Chem. Inf. Model. 2015, 55 (7) 1495-1507 10.1021/acs.jcim.5b00082
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.7
, pp. 1495-1507
-
-
Krull, F.1
Korff, G.2
Elghobashi-Meinhardt, N.3
Knapp, E.W.4
-
3
-
-
84920462422
-
Rational Design of Protein-Protein Interaction Inhibitors
-
Rognan, D. Rational Design of Protein-Protein Interaction Inhibitors MedChemComm 2015, 6 (1) 51-60 10.1039/C4MD00328D
-
(2015)
MedChemComm
, vol.6
, Issue.1
, pp. 51-60
-
-
Rognan, D.1
-
4
-
-
84960331999
-
Stabilization of Protein-Protein Interaction Complexes Through Small Molecules
-
Zarzycka, B.; Kuenemann, M. A.; Miteva, M. A.; Nicolaes, G. A. F.; Vriend, G.; Sperandio, O. Stabilization of Protein-Protein Interaction Complexes Through Small Molecules Drug Discovery Today 2016, 21 (1) 48-57 10.1016/j.drudis.2015.09.011
-
(2016)
Drug Discovery Today
, vol.21
, Issue.1
, pp. 48-57
-
-
Zarzycka, B.1
Kuenemann, M.A.2
Miteva, M.A.3
Nicolaes, G.A.F.4
Vriend, G.5
Sperandio, O.6
-
5
-
-
84976865397
-
IPPI-DB: An Online Database of Modulators of Protein-Protein Interactions
-
Labbe, C. M.; Kuenemann, M. A.; Zarzycka, B.; Vriend, G.; Nicolaes, G. A.; Lagorce, D.; Miteva, M. A.; Villoutreix, B. O.; Sperandio, O. iPPI-DB: An Online Database of Modulators of Protein-Protein Interactions Nucleic Acids Res. 2016, 44 (D1) D542-547 10.1093/nar/gkv982
-
(2016)
Nucleic Acids Res.
, vol.44
, Issue.D1
, pp. D542-D547
-
-
Labbe, C.M.1
Kuenemann, M.A.2
Zarzycka, B.3
Vriend, G.4
Nicolaes, G.A.5
Lagorce, D.6
Miteva, M.A.7
Villoutreix, B.O.8
Sperandio, O.9
-
6
-
-
84899975034
-
Discovery of 14-3-3 Protein- Protein Interaction Inhibitors that Sensitize Multidrug-Resistant Cancer Cells to Doxorubicin and the Akt Inhibitor GSK690693
-
Mori, M.; Vignaroli, G.; Cau, Y.; Dinic, J.; Hill, R.; Rossi, M.; Colecchia, D.; Pesic, M.; Link, W.; Chiariello, M.; Ottmann, C.; Botta, M. Discovery of 14-3-3 Protein- Protein Interaction Inhibitors that Sensitize Multidrug-Resistant Cancer Cells to Doxorubicin and the Akt Inhibitor GSK690693 ChemMedChem 2014, 9 (5) 973-983 10.1002/cmdc.201400044
-
(2014)
ChemMedChem
, vol.9
, Issue.5
, pp. 973-983
-
-
Mori, M.1
Vignaroli, G.2
Cau, Y.3
Dinic, J.4
Hill, R.5
Rossi, M.6
Colecchia, D.7
Pesic, M.8
Link, W.9
Chiariello, M.10
Ottmann, C.11
Botta, M.12
-
7
-
-
84923377424
-
Discovery of Small Molecule CD40-TRAF6 Inhibitors
-
Zarzycka, B.; Seijkens, T.; Nabuurs, S. B.; Ritschel, T.; Grommes, J.; Soehnlein, O.; Schrijver, R.; van Tiel, C. M.; Hackeng, T. M.; Weber, C.; Giehler, F.; Kieser, A.; Lutgens, E.; Vriend, G.; Nicolaes, G. A. F. Discovery of Small Molecule CD40-TRAF6 Inhibitors J. Chem. Inf. Model. 2015, 55 (2) 294-307 10.1021/ci500631e
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.2
, pp. 294-307
-
-
Zarzycka, B.1
Seijkens, T.2
Nabuurs, S.B.3
Ritschel, T.4
Grommes, J.5
Soehnlein, O.6
Schrijver, R.7
Van Tiel, C.M.8
Hackeng, T.M.9
Weber, C.10
Giehler, F.11
Kieser, A.12
Lutgens, E.13
Vriend, G.14
Nicolaes, G.A.F.15
-
8
-
-
84900503009
-
Identification of Novel Small Molecule Inhibitors of Activated Protein C
-
Sperandio, O.; Wildhagen, K. C. A. A.; Schrijver, R.; Wielders, S.; Villoutreix, B. O.; Nicolaes, G. A. F. Identification of Novel Small Molecule Inhibitors of Activated Protein C Thromb. Res. 2014, 133 (6) 1105-1114 10.1016/j.thromres.2014.01.026
-
(2014)
Thromb. Res.
, vol.133
, Issue.6
, pp. 1105-1114
-
-
Sperandio, O.1
Wildhagen, K.C.A.A.2
Schrijver, R.3
Wielders, S.4
Villoutreix, B.O.5
Nicolaes, G.A.F.6
-
9
-
-
84875436143
-
Inhibition of Alpha-Helix-Mediated Protein-Protein Interactions Using Designed Molecules
-
Azzarito, V.; Long, K.; Murphy, N. S.; Wilson, A. J. Inhibition of Alpha-Helix-Mediated Protein-Protein Interactions Using Designed Molecules Nat. Chem. 2013, 5 (3) 161-173 10.1038/nchem.1568
-
(2013)
Nat. Chem.
, vol.5
, Issue.3
, pp. 161-173
-
-
Azzarito, V.1
Long, K.2
Murphy, N.S.3
Wilson, A.J.4
-
10
-
-
84894447457
-
Rational Design of Small Molecules Targeting the C2 Domain of Coagulation Factor VIII
-
Nicolaes, G. A. F.; Kulharia, M.; Voorberg, J.; Kaijen, P. H.; Wroblewska, A.; Wielders, S.; Schrijver, R.; Sperandio, O.; Villoutreix, B. O. Rational Design of Small Molecules Targeting the C2 Domain of Coagulation Factor VIII Blood 2014, 123 (1) 113-120 10.1182/blood-2013-05-503227
-
(2014)
Blood
, vol.123
, Issue.1
, pp. 113-120
-
-
Nicolaes, G.A.F.1
Kulharia, M.2
Voorberg, J.3
Kaijen, P.H.4
Wroblewska, A.5
Wielders, S.6
Schrijver, R.7
Sperandio, O.8
Villoutreix, B.O.9
-
11
-
-
84922470425
-
Molecular Simulation Studies of Human Coagulation Factor VIII C Domain-Mediated Membrane Binding
-
Du, J. F.; Wichapong, K.; Hackeng, T. M.; Nicolaes, G. A. F. Molecular Simulation Studies of Human Coagulation Factor VIII C Domain-Mediated Membrane Binding Thromb. Haemostasis 2015, 113 (2) 373-384 10.1160/TH14-02-0180
-
(2015)
Thromb. Haemostasis
, vol.113
, Issue.2
, pp. 373-384
-
-
Du, J.F.1
Wichapong, K.2
Hackeng, T.M.3
Nicolaes, G.A.F.4
-
12
-
-
84855675652
-
In Vitro and in Silico Studies on Substrate Recognition and Acceptance of Human PKMYT1, a Cdk1 Inhibitory Kinase
-
Rohe, A.; Erdmann, F.; Bassler, C.; Wichapong, K.; Sippl, W.; Schmidt, M. In Vitro and In Silico Studies on Substrate Recognition and Acceptance of Human PKMYT1, a Cdk1 Inhibitory Kinase Bioorg. Med. Chem. Lett. 2012, 22 (2) 1219-1223 10.1016/j.bmcl.2011.11.064
-
(2012)
Bioorg. Med. Chem. Lett.
, vol.22
, Issue.2
, pp. 1219-1223
-
-
Rohe, A.1
Erdmann, F.2
Bassler, C.3
Wichapong, K.4
Sippl, W.5
Schmidt, M.6
-
13
-
-
79960007037
-
Complete Reconstruction of an Enzyme-Inhibitor Binding Process by Molecular Dynamics Simulations
-
Buch, I.; Giorgino, T.; De Fabritiis, G. Complete Reconstruction of an Enzyme-Inhibitor Binding Process by Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (25) 10184-10189 10.1073/pnas.1103547108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.25
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
14
-
-
79959275847
-
How Does a Drug Molecule Find Its Target Binding Site?
-
Shan, Y. B.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. How Does a Drug Molecule Find Its Target Binding Site? J. Am. Chem. Soc. 2011, 133 (24) 9181-9183 10.1021/ja202726y
-
(2011)
J. Am. Chem. Soc.
, vol.133
, Issue.24
, pp. 9181-9183
-
-
Shan, Y.B.1
Kim, E.T.2
Eastwood, M.P.3
Dror, R.O.4
Seeliger, M.A.5
Shaw, D.E.6
-
15
-
-
84923096526
-
The Ligand Binding Mechanism to Purine Nucleoside Phosphorylase Elucidated via Molecular Dynamics and Machine Learning
-
Decherchi, S.; Berteotti, A.; Bottegoni, G.; Rocchia, W.; Cavalli, A. The Ligand Binding Mechanism to Purine Nucleoside Phosphorylase Elucidated via Molecular Dynamics and Machine Learning Nat. Commun. 2015, 6, 6155 10.1038/ncomms7155
-
(2015)
Nat. Commun.
, vol.6
, pp. 6155
-
-
Decherchi, S.1
Berteotti, A.2
Bottegoni, G.3
Rocchia, W.4
Cavalli, A.5
-
16
-
-
0034811498
-
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by docking and MM-PBSA
-
Wang, J. M.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz By docking and MM-PBSA J. Am. Chem. Soc. 2001, 123 (22) 5221-5230 10.1021/ja003834q
-
(2001)
J. Am. Chem. Soc.
, vol.123
, Issue.22
, pp. 5221-5230
-
-
Wang, J.M.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
17
-
-
84896961990
-
Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors
-
Wichapong, K.; Rohe, A.; Platzer, C.; Slynko, I.; Erdmann, F.; Schmidt, M.; Sippl, W. Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors J. Chem. Inf. Model. 2014, 54 (3) 881-893 10.1021/ci4007326
-
(2014)
J. Chem. Inf. Model.
, vol.54
, Issue.3
, pp. 881-893
-
-
Wichapong, K.1
Rohe, A.2
Platzer, C.3
Slynko, I.4
Erdmann, F.5
Schmidt, M.6
Sippl, W.7
-
18
-
-
84893425548
-
Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development
-
Slynko, I.; Scharfe, M.; Rumpf, T.; Eib, J.; Metzger, E.; Schule, R.; Jung, M.; Sippl, W. Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development J. Chem. Inf. Model. 2014, 54 (1) 138-150 10.1021/ci400628q
-
(2014)
J. Chem. Inf. Model.
, vol.54
, Issue.1
, pp. 138-150
-
-
Slynko, I.1
Scharfe, M.2
Rumpf, T.3
Eib, J.4
Metzger, E.5
Schule, R.6
Jung, M.7
Sippl, W.8
-
19
-
-
84924248243
-
Docking and Binding Free Energy Calculations of Sirtuin Inhibitors
-
Karaman, B.; Sippl, W. Docking and Binding Free Energy Calculations of Sirtuin Inhibitors Eur. J. Med. Chem. 2015, 93, 584-598 10.1016/j.ejmech.2015.02.045
-
(2015)
Eur. J. Med. Chem.
, vol.93
, pp. 584-598
-
-
Karaman, B.1
Sippl, W.2
-
20
-
-
84872166189
-
Leukocyte Behavior in Atherosclerosis, Myocardial Infarction, and Heart Failure
-
Swirski, F. K.; Nahrendorf, M. Leukocyte Behavior in Atherosclerosis, Myocardial Infarction, and Heart Failure Science 2013, 339 (6116) 161-166 10.1126/science.1230719
-
(2013)
Science
, vol.339
, Issue.6116
, pp. 161-166
-
-
Swirski, F.K.1
Nahrendorf, M.2
-
21
-
-
84874729375
-
Distinct Functions of Chemokine Receptor Axes in the Atherogenic Mobilization and Recruitment of Classical Monocytes
-
Soehnlein, O.; Drechsler, M.; Doring, Y.; Lievens, D.; Hartwig, H.; Kemmerich, K.; Ortega-Gomez, A.; Mandl, M.; Vijayan, S.; Projahn, D.; Garlichs, C. D.; Koenen, R. R.; Hristov, M.; Lutgens, E.; Zernecke, A.; Weber, C. Distinct Functions of Chemokine Receptor Axes in the Atherogenic Mobilization and Recruitment of Classical Monocytes EMBO. Mol. Med. 2013, 5 (3) 471-481 10.1002/emmm.201201717
-
(2013)
EMBO. Mol. Med.
, vol.5
, Issue.3
, pp. 471-481
-
-
Soehnlein, O.1
Drechsler, M.2
Doring, Y.3
Lievens, D.4
Hartwig, H.5
Kemmerich, K.6
Ortega-Gomez, A.7
Mandl, M.8
Vijayan, S.9
Projahn, D.10
Garlichs, C.D.11
Koenen, R.R.12
Hristov, M.13
Lutgens, E.14
Zernecke, A.15
Weber, C.16
-
22
-
-
52949118458
-
Harmful Molecular Mechanisms in Sepsis
-
Rittirsch, D.; Flierl, M. A.; Ward, P. A. Harmful Molecular Mechanisms in Sepsis Nat. Rev. Immunol. 2008, 8 (10) 776-787 10.1038/nri2402
-
(2008)
Nat. Rev. Immunol.
, vol.8
, Issue.10
, pp. 776-787
-
-
Rittirsch, D.1
Flierl, M.A.2
Ward, P.A.3
-
23
-
-
73949096361
-
Mechanisms Underlying Neutrophil-Mediated Monocyte Recruitment
-
Soehnlein, O.; Lindbom, L.; Weber, C. Mechanisms Underlying Neutrophil-Mediated Monocyte Recruitment Blood 2009, 114 (21) 4613-4623 10.1182/blood-2009-06-221630
-
(2009)
Blood
, vol.114
, Issue.21
, pp. 4613-4623
-
-
Soehnlein, O.1
Lindbom, L.2
Weber, C.3
-
24
-
-
51649104412
-
Neutrophil Secretion Products Pave the Way for Inflammatory Monocytes
-
Soehnlein, O.; Zernecke, A.; Eriksson, E. E.; Rothfuchs, A. G.; Pham, C. T.; Herwald, H.; BidzhekoV, K.; Rottenberg, M. E.; Weber, C.; Lindbom, L. Neutrophil Secretion Products Pave the Way for Inflammatory Monocytes Blood 2008, 112 (4) 1461-1471 10.1182/blood-2008-02-139634
-
(2008)
Blood
, vol.112
, Issue.4
, pp. 1461-1471
-
-
Soehnlein, O.1
Zernecke, A.2
Eriksson, E.E.3
Rothfuchs, A.G.4
Pham, C.T.5
Herwald, H.6
BidzhekoV, K.7
Rottenberg, M.E.8
Weber, C.9
Lindbom, L.10
-
25
-
-
84954431664
-
Recruitment of Classical Monocytes can be Inhibited by Disturbing Heteromers of Neutrophil HNP1 and Platelet CCL5
-
Alard, J.-E.; Ortega-Gomez, A.; Wichapong, K.; Bongiovanni, D.; Horckmans, M.; Megens, R. T. A.; Leoni, G.; Ferraro, B.; Rossaint, J.; Paulin, N.; Ng, J.; Ippel, H.; Suylen, D.; Hinkel, R.; Blanchet, X.; Gaillard, F.; DAmico, M.; von Hundelshausen, P.; Zarbock, A.; Scheiermann, C.; Hackeng, T. M.; Steffens, S.; Kupatt, C.; Nicolaes, G. A. F.; Weber, C.; Soehnlein, O. Recruitment of Classical Monocytes can be Inhibited by Disturbing Heteromers of Neutrophil HNP1 and Platelet CCL5 Sci. Transl. Med. 2015, 7 (317) 317ra196 10.1126/scitranslmed.aad5330
-
(2015)
Sci. Transl. Med.
, vol.7
, Issue.317
, pp. 317ra196
-
-
Alard, J.-E.1
Ortega-Gomez, A.2
Wichapong, K.3
Bongiovanni, D.4
Horckmans, M.5
Megens, R.T.A.6
Leoni, G.7
Ferraro, B.8
Rossaint, J.9
Paulin, N.10
Ng, J.11
Ippel, H.12
Suylen, D.13
Hinkel, R.14
Blanchet, X.15
Gaillard, F.16
D'Amico, M.17
Von Hundelshausen, P.18
Zarbock, A.19
Scheiermann, C.20
Hackeng, T.M.21
Steffens, S.22
Kupatt, C.23
Nicolaes, G.A.F.24
Weber, C.25
Soehnlein, O.26
more..
-
26
-
-
84898455342
-
Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity
-
Li, M. H.; Petukh, M.; Alexov, E.; Panchenko, A. R. Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity J. Chem. Theory Comput. 2014, 10 (4) 1770-1780 10.1021/ct401022c
-
(2014)
J. Chem. Theory Comput.
, vol.10
, Issue.4
, pp. 1770-1780
-
-
Li, M.H.1
Petukh, M.2
Alexov, E.3
Panchenko, A.R.4
-
27
-
-
80054900286
-
Protein-Protein Binding Affinity Prediction on a Diverse Set of Structures
-
Moal, I. H.; Agius, R.; Bates, P. A. Protein-Protein Binding Affinity Prediction on a Diverse Set of Structures Bioinformatics 2011, 27 (21) 3002-3009 10.1093/bioinformatics/btr513
-
(2011)
Bioinformatics
, vol.27
, Issue.21
, pp. 3002-3009
-
-
Moal, I.H.1
Agius, R.2
Bates, P.A.3
-
28
-
-
84857428250
-
Prediction of Protein-Protein Binding Free Energies
-
Vreven, T.; Hwang, H.; Pierce, B. G.; Weng, Z. Prediction of Protein-Protein Binding Free Energies Protein Sci. 2012, 21 (3) 396-404 10.1002/pro.2027
-
(2012)
Protein Sci.
, vol.21
, Issue.3
, pp. 396-404
-
-
Vreven, T.1
Hwang, H.2
Pierce, B.G.3
Weng, Z.4
-
29
-
-
84923567004
-
Analysis of the Resistance of Hepatitis C Virus NS5B Polymerase Inhibitors via Docking and Molecular Dynamics Simulation
-
Uengwetwanit, T.; Robaa, D.; Sippl, W. Analysis of the Resistance of Hepatitis C Virus NS5B Polymerase Inhibitors via Docking and Molecular Dynamics Simulation Mol. Inf. 2015, 34 (2-3) 78-83 10.1002/minf.201400048
-
(2015)
Mol. Inf.
, vol.34
, Issue.23
, pp. 78-83
-
-
Uengwetwanit, T.1
Robaa, D.2
Sippl, W.3
-
30
-
-
0034995775
-
The Pan-Chemokine Inhibitor NR58-3.14.3 Abolishes Tumour Necrosis Factor-Alpha Accumulation and Leucocyte Recruitment Induced by Lipopolysaccharide in Vivo
-
Reckless, J.; Tatalick, L. M.; Grainger, D. J. The Pan-Chemokine Inhibitor NR58-3.14.3 Abolishes Tumour Necrosis Factor-Alpha Accumulation and Leucocyte Recruitment Induced by Lipopolysaccharide In Vivo Immunology 2001, 103 (2) 244-254 10.1046/j.1365-2567.2001.01228.x
-
(2001)
Immunology
, vol.103
, Issue.2
, pp. 244-254
-
-
Reckless, J.1
Tatalick, L.M.2
Grainger, D.J.3
-
31
-
-
37249062877
-
-
version 4.0; Accelrys Software Inc: San Diego, CA
-
Discovery Studio, version 4.0; Accelrys Software Inc: San Diego, CA, 2010.
-
(2010)
Discovery Studio
-
-
-
32
-
-
84945207209
-
Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design
-
Xie, N. Z.; Du, Q. S.; Li, J. X.; Huang, R. B. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design PLoS One 2015, 10 (9) e0137113 10.1371/journal.pone.0137113
-
(2015)
PLoS One
, vol.10
, Issue.9
, pp. e0137113
-
-
Xie, N.Z.1
Du, Q.S.2
Li, J.X.3
Huang, R.B.4
-
33
-
-
84962463344
-
Theoretical Study on the Polar Hydrogen-Pi (Hp-Pi) Interactions between Protein Side Chains
-
Du, Q. S.; Wang, Q. Y.; Du, L. Q.; Chen, D.; Huang, R. B. Theoretical Study on the Polar Hydrogen-Pi (Hp-Pi) Interactions between Protein Side Chains Chem. Cent. J. 2013, 7, 92 10.1186/1752-153X-7-92
-
(2013)
Chem. Cent. J.
, vol.7
, pp. 92
-
-
Du, Q.S.1
Wang, Q.Y.2
Du, L.Q.3
Chen, D.4
Huang, R.B.5
-
34
-
-
84962417597
-
Unconventional Interaction Forces in Protein and Protein-Ligand Systems and Their Impacts to Drug Design
-
Wang, Q. Y.; Lu, J.; Liao, S. M.; Du, Q. S.; Huang, R. B. Unconventional Interaction Forces in Protein and Protein-Ligand Systems and Their Impacts to Drug Design Curr. Top. Med. Chem. 2013, 13 (10) 1141-1151 10.2174/15680266113139990002
-
(2013)
Curr. Top. Med. Chem.
, vol.13
, Issue.10
, pp. 1141-1151
-
-
Wang, Q.Y.1
Lu, J.2
Liao, S.M.3
Du, Q.S.4
Huang, R.B.5
-
35
-
-
84986522918
-
ICM - A New Method for Protein Modeling and Design - Applications to Docking and Structure Prediction from the Distorted Native Conformation
-
Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM-a New Method for Protein Modeling and Design-Applications to Docking and Structure Prediction from the Distorted Native Conformation J. Comput. Chem. 1994, 15 (5) 488-506 10.1002/jcc.540150503
-
(1994)
J. Comput. Chem.
, vol.15
, Issue.5
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
36
-
-
32144432437
-
The SWISS-MODEL Workspace: A Web-Based Environment for Protein Structure Homology Modelling
-
Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL Workspace: A Web-Based Environment for Protein Structure Homology Modelling Bioinformatics 2006, 22 (2) 195-201 10.1093/bioinformatics/bti770
-
(2006)
Bioinformatics
, vol.22
, Issue.2
, pp. 195-201
-
-
Arnold, K.1
Bordoli, L.2
Kopp, J.3
Schwede, T.4
-
37
-
-
0030047142
-
Errors in Protein Structures
-
Hooft, R. W. W.; Vriend, G.; Sander, C.; Abola, E. E. Errors in Protein Structures Nature 1996, 381 (6580) 272-272 10.1038/381272a0
-
(1996)
Nature
, vol.381
, Issue.6580
, pp. 272
-
-
Hooft, R.W.W.1
Vriend, G.2
Sander, C.3
Abola, E.E.4
-
38
-
-
84862614975
-
-
University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Götz, A. W.; KolossvaÌry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 12; University of California: San Francisco, 2012.
-
(2012)
AMBER 12
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Hayik, S.12
Roitberg, A.13
Seabra, G.14
Swails, J.15
Götz, A.W.16
Kolossvaìry, I.17
Wong, K.F.18
Paesani, F.19
Vanicek, J.20
Wolf, R.M.21
Liu, J.22
Wu, X.23
Brozell, S.R.24
Steinbrecher, T.25
Gohlke, H.26
Cai, Q.27
Ye, X.28
Wang, J.29
Hsieh, M.-J.30
Cui, G.31
Roe, D.R.32
Mathews, D.H.33
Seetin, M.G.34
Salomon-Ferrer, R.35
Sagui, C.36
Babin, V.37
Luchko, T.38
Gusarov, S.39
Kovalenko, A.40
Kollman, P.A.41
more..
-
39
-
-
33748518255
-
Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins: Struct., Funct., Genet. 2006, 65 (3) 712-725 10.1002/prot.21123
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
40
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79 (2) 926-935 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
41
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes J. Comput. Phys. 1977, 23 (3) 327-341 10.1016/0021-9991(77)90098-5
-
(1977)
J. Comput. Phys.
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
42
-
-
33846823909
-
Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98 (12) 10089-10092 10.1063/1.464397
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
43
-
-
76249112547
-
Fast and Accurate Predictions of Binding Free Energies Using MM-PBSA and MM-GBSA
-
Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and Accurate Predictions of Binding Free Energies Using MM-PBSA and MM-GBSA J. Comput. Chem. 2010, 31 (4) 797-810 10.1002/jcc.21372
-
(2010)
J. Comput. Chem.
, vol.31
, Issue.4
, pp. 797-810
-
-
Rastelli, G.1
Del Rio, A.2
Degliesposti, G.3
Sgobba, M.4
-
44
-
-
77957242467
-
Postprocessing of Protein-Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors
-
Wichapong, K.; Lawson, M.; Pianwanit, S.; Kokpol, S.; Sippl, W. Postprocessing of Protein-Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors J. Chem. Inf. Model. 2010, 50 (9) 1574-1588 10.1021/ci1002153
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.9
, pp. 1574-1588
-
-
Wichapong, K.1
Lawson, M.2
Pianwanit, S.3
Kokpol, S.4
Sippl, W.5
-
45
-
-
33750467966
-
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
-
Weis, A.; Katebzadeh, K.; Soderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field J. Med. Chem. 2006, 49 (22) 6596-6606 10.1021/jm0608210
-
(2006)
J. Med. Chem.
, vol.49
, Issue.22
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Soderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
46
-
-
79952127760
-
Postprocessing of Docked Protein-Ligand Complexes Using Implicit Solvation Models
-
Lindstrom, A.; Edvinsson, L.; Johansson, A.; Andersson, C. D.; Andersson, I. E.; Raubacher, F.; Linusson, A. Postprocessing of Docked Protein-Ligand Complexes Using Implicit Solvation Models J. Chem. Inf. Model. 2011, 51 (2) 267-282 10.1021/ci100354x
-
(2011)
J. Chem. Inf. Model.
, vol.51
, Issue.2
, pp. 267-282
-
-
Lindstrom, A.1
Edvinsson, L.2
Johansson, A.3
Andersson, C.D.4
Andersson, I.E.5
Raubacher, F.6
Linusson, A.7
-
47
-
-
60349105674
-
Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening
-
Rastelli, G.; Degliesposti, G.; Del Rio, A.; Sgobba, M. Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening Chem. Biol. Drug Des. 2009, 73 (3) 283-286 10.1111/j.1747-0285.2009.00780.x
-
(2009)
Chem. Biol. Drug Des.
, vol.73
, Issue.3
, pp. 283-286
-
-
Rastelli, G.1
Degliesposti, G.2
Del Rio, A.3
Sgobba, M.4
-
48
-
-
84866167816
-
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
-
Miller, B. R.; McGee, T. D.; Swails, J. M.; Homeyer, N.; Gohlke, H.; Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations J. Chem. Theory Comput. 2012, 8 (9) 3314-3321 10.1021/ct300418h
-
(2012)
J. Chem. Theory Comput.
, vol.8
, Issue.9
, pp. 3314-3321
-
-
Miller, B.R.1
McGee, T.D.2
Swails, J.M.3
Homeyer, N.4
Gohlke, H.5
Roitberg, A.E.6
-
49
-
-
84857245894
-
Binding Free Energy Calculations and Biological Testing of Novel Thiobarbiturates as Inhibitors of the Human NAD(+) Dependent Histone Deacetylase Sirt2
-
Uciechowska, U.; Schemies, J.; Scharfe, M.; Lawson, M.; Wichapong, K.; Jung, M.; Sippl, W. Binding Free Energy Calculations and Biological Testing of Novel Thiobarbiturates as Inhibitors of The Human NAD(+) Dependent Histone Deacetylase Sirt2 MedChemComm 2012, 3 (2) 167-173 10.1039/C1MD00214G
-
(2012)
MedChemComm
, vol.3
, Issue.2
, pp. 167-173
-
-
Uciechowska, U.1
Schemies, J.2
Scharfe, M.3
Lawson, M.4
Wichapong, K.5
Jung, M.6
Sippl, W.7
-
50
-
-
41649096077
-
Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model
-
Kolb, P.; Huang, D.; Dey, F.; Caflisch, A. Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model J. Med. Chem. 2008, 51 (5) 1179-1188 10.1021/jm070654j
-
(2008)
J. Med. Chem.
, vol.51
, Issue.5
, pp. 1179-1188
-
-
Kolb, P.1
Huang, D.2
Dey, F.3
Caflisch, A.4
-
51
-
-
58149336758
-
Disrupting Functional Interactions between Platelet Chemokines Inhibits Atherosclerosis in Hyperlipidemic Mice
-
Koenen, R. R.; von Hundelshausen, P.; Nesmelova, I. V.; Zernecke, A.; Liehn, E. A.; Sarabi, A.; Kramp, B. K.; Piccinini, A. M.; Paludan, S. R.; Kowalska, M. A.; Kungl, A. J.; Hackeng, T. M.; Mayo, K. H.; Weber, C. Disrupting Functional Interactions between Platelet Chemokines Inhibits Atherosclerosis in Hyperlipidemic Mice Nat. Med. 2009, 15 (1) 97-103 10.1038/nm.1898
-
(2009)
Nat. Med.
, vol.15
, Issue.1
, pp. 97-103
-
-
Koenen, R.R.1
Von Hundelshausen, P.2
Nesmelova, I.V.3
Zernecke, A.4
Liehn, E.A.5
Sarabi, A.6
Kramp, B.K.7
Piccinini, A.M.8
Paludan, S.R.9
Kowalska, M.A.10
Kungl, A.J.11
Hackeng, T.M.12
Mayo, K.H.13
Weber, C.14
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