-
2
-
-
33144467064
-
Electrostatic influence of PsaC protein binding to the PsaA/PsaB heterodimer in photosystem i
-
Ishikita H, Stehlik D, Golbeck JH, Knapp EW (2006) Electrostatic influence of PsaC protein binding to the PsaA/PsaB heterodimer in photosystem I. Biophys. J. 90: 1081-1089
-
(2006)
Biophys. J.
, vol.90
, pp. 1081-1089
-
-
Ishikita, H.1
Stehlik, D.2
Golbeck, J.H.3
Knapp, E.W.4
-
3
-
-
0030442990
-
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
-
DOI 10.1002/(SICI)1097-0134(199612)26:4<363::AID-PROT1>3.0.CO;2-D
-
Hooft RWW, Sander C, Vriend G (1996) Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 26: 363-376 (Pubitemid 27024754)
-
(1996)
Proteins: Structure, Function and Genetics
, vol.26
, Issue.4
, pp. 363-376
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
4
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
DOI 10.1006/jmbi.1998.2401
-
Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285: 1735-1747 (Pubitemid 29060467)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
5
-
-
58149476769
-
Pace CN A summary of the measured pK values of the ionizable groups in folded proteins
-
Grimsley GR, Scholtz JM, Pace CN A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci. 18: 247-251
-
Protein Sci
, vol.18
, pp. 247-251
-
-
Grimsley, G.R.1
Scholtz, J.M.2
-
6
-
-
0032586777
-
Simplified methods for pK(a) and acid pH-dependent stability estimation in proteins: Removing dielectric and counterion boundaries
-
Warwicker J (1999) Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries. Protein Sci. 8: 418-425 (Pubitemid 29072442)
-
(1999)
Protein Science
, vol.8
, Issue.2
, pp. 418-425
-
-
Warwicker, J.1
-
7
-
-
0032769471
-
A fast and simple method to calculate protonation states in proteins
-
DOI 10.1002/(SICI)1097-0134(19990901)36:4<474::AID-PROT12>3.0.CO;2- V
-
Sandberg L, Edholm O (1999) A fast and simple method to calculate protonation states in proteins. Proteins 36: 474-483 (Pubitemid 29387747)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.36
, Issue.4
, pp. 474-483
-
-
Sandberg, L.1
Edholm, O.2
-
8
-
-
0020475509
-
Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
-
Warwicker J, Watson HC (1982) Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 157: 671-679
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
9
-
-
0027563464
-
-
Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B (1993) On the calculation of pKas in proteins. 15: 252-265
-
(1993)
On the Calculation of PKas in Proteins.
, vol.15
, pp. 252-265
-
-
Yang, A.S.1
Gunner, M.R.2
Sampogna, R.3
Sharp, K.4
Honig, B.5
-
11
-
-
33749021099
-
a values of functional groups in protein-ligand complexes
-
DOI 10.1002/prot.21110
-
Czodrowski P, Dramburg I, Sotriffer CA, Klebe G (2006) Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins 65: 424-437 (Pubitemid 44454114)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.2
, pp. 424-437
-
-
Czodrowski, P.1
Dramburg, I.2
Sotriffer, C.A.3
Klebe, G.4
-
12
-
-
33750528726
-
a prediction by Ewald summation
-
DOI 10.1016/j.jmgm.2006.02.009, PII S1093326306000477
-
KriegerE, Nielsen JE, SpronkCAEM, VriendG (2006) Fast empirical pKa prediction by Ewald summation. JMol Graph Model 25: 481-486 (Pubitemid 44667584)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.4
, pp. 481-486
-
-
Krieger, E.1
Nielsen, J.E.2
Spronk, C.A.E.M.3
Vriend, G.4
-
14
-
-
56449089334
-
PKa prediction of monoprotic small molecules the SMARTS way
-
Lee AC, Yu JY, Crippen GM (2008) pKa prediction of monoprotic small molecules the SMARTS way. J. Chem. Inf.Model. 48: 2043-2053
-
(2008)
J. Chem. Inf.Model.
, vol.48
, pp. 2043-2053
-
-
Lee, A.C.1
Yu, J.Y.2
Crippen, G.M.3
-
15
-
-
72449138105
-
In silico pKa prediction and ADME profiling
-
Cruciani G, Milletti F, Storchi L, Sforna G, Goracci L (2009) In silico pKa prediction and ADME profiling. Chem. Biodivers. 6: 1812-1821
-
(2009)
Chem. Biodivers.
, vol.6
, pp. 1812-1821
-
-
Cruciani, G.1
Milletti, F.2
Storchi, L.3
Sforna, G.4
Goracci, L.5
-
16
-
-
33745599120
-
NQ-Flipper: Validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
-
DOI 10.1093/bioinformatics/btl128
-
Weichenberger CX, Sippl MJ (2006) NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. Bioinformatics 22: 1397-1398 (Pubitemid 43985277)
-
(2006)
Bioinformatics
, vol.22
, Issue.11
, pp. 1397-1398
-
-
Weichenberger, C.X.1
Sippl, M.J.2
-
17
-
-
74049110393
-
Fast automated placement of polar hydrogen atoms in protein-ligand complexes
-
Lippert T, Rarey M (2009) Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J.Cheminform. 1: 13
-
(2009)
J.Cheminform.
, vol.1
, pp. 13
-
-
Lippert, T.1
Rarey, M.2
-
18
-
-
0023965741
-
SMILES, a chemical language and information system
-
Weininger D (1993) SMILES, a chemical language and information system. J. Chem. Inf. Comput.Sci 28: 31-36
-
(1993)
J. Chem. Inf. Comput.Sci
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
19
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
DOI 10.1110/ps.03154503
-
Canutescu AA, Shelenkov AA, Dunbrack RLJ (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12: 2001-2014 (Pubitemid 37022822)
-
(2003)
Protein Science
, vol.12
, Issue.9
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack Jr., R.L.3
-
20
-
-
26444443482
-
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures
-
DOI 10.1002/prot.20601
-
Forrest LR, Honig B (2005) An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins: 296-309 (Pubitemid 41429137)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.2
, pp. 296-309
-
-
Forrest, L.R.1
Honig, B.2
-
21
-
-
77955660371
-
A Point-charge force field for molecular mechanics simulations of proteins
-
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T (2003) A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins. J. Comp. Chem. 24: 1999-2012
-
(2003)
J. Comp. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan Ywu, C.1
Chowdhury, S.2
Lee, M.C.3
Xiong, G.4
Zhang, W.5
Yang, R.6
Cieplak, P.7
Luo, R.8
Lee, T.9
-
22
-
-
2942532422
-
Development and testing of a general AMBER force field
-
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general AMBER force field. J.Comp. Chem. 25: 1157-1174
-
(2004)
J.Comp. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
23
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCCmodel: II. Parameterization and validation. J.Comput. Chem. 23: 1623-1641 (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
24
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
-
Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph.Model. 25: 247-260 (Pubitemid 44363172)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.2
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
25
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35: W522-W525
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
-
26
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essman U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essman, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
27
-
-
0036783381
-
Variability in the pKa of histidine side-chains correlates with burial within proteins
-
DOI 10.1002/prot.10177
-
Edgcomb SP, Murphy PM (2002) Variability in the pKa of histidine side-chains correlates with burial within proteins. Proteins 49: 1-6 (Pubitemid 34983169)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.49
, Issue.1
, pp. 1-6
-
-
Edgcomb, S.P.1
Murphy, K.P.2
-
28
-
-
77955552577
-
Extending pKa prediction accuracy: Highthroughput pKa measurements to understand pKa modulation of new chemical series
-
Milletti F, Storchi L, Goracci L, Bendels S, Wagner B, Kansy M, Cruciani G (2010) Extending pKa prediction accuracy: highthroughput pKa measurements to understand pKa modulation of new chemical series. Eur. J. Med. Chem. 45: 4270-4279
-
(2010)
Eur. J. Med. Chem.
, Issue.45
, pp. 4270-4279
-
-
Milletti, F.1
Storchi, L.2
Goracci, L.3
Bendels, S.4
Wagner, B.5
Kansy, M.6
Cruciani, G.7
-
29
-
-
0030564892
-
Helmholtz free energy of peptide hydrogen bonds in proteins
-
DOI 10.1006/jmbi.1996.0427
-
Sippl MJ (1996) Helmholtz free energy of peptide hydrogen bonds in proteins. J. Mol. Biol. 260: 644-648 (Pubitemid 26270959)
-
(1996)
Journal of Molecular Biology
, vol.260
, Issue.5
, pp. 644-648
-
-
Sippl, M.J.1
-
30
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly ML (1983) Analytical molecular surface calculation. J.Appl.Cryst. 16: 548-558
-
(1983)
J.Appl.Cryst.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
32
-
-
0037305552
-
On the evaluation and optimization of protein X-ray structures for pKa calculations
-
DOI 10.1110/ps.0229903
-
Nielsen JE, McCammon JA (2003) On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci. 12: 313-326 (Pubitemid 36120344)
-
(2003)
Protein Science
, vol.12
, Issue.2
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
|