-
1
-
-
0002638513
-
Protein data bank
-
Allen, F.H., Bergerhoff, G. & Sievers, R., eds, Data Commission of the International Union of Crystallography, Bonn, Germany
-
Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. & Weng, J. (1987). Protein data bank. In Crystallographic databases-information content, software systems, scientific applications. (Allen, F.H., Bergerhoff, G. & Sievers, R., eds), pp. 107-132. Data Commission of the International Union of Crystallography, Bonn, Germany.
-
(1987)
Crystallographic Databases-information Content, Software Systems, Scientific Applications
, pp. 107-132
-
-
Abola, E.E.1
Bernstein, F.C.2
Bryant, S.H.3
Koetzle, T.F.4
Weng, J.5
-
2
-
-
0026055156
-
Analysis of the steric strain in the polypeptide backbone of protein molecules
-
Herzberg, O. & Moult, J. (1991). Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins 11, 223-229.
-
(1991)
Proteins
, vol.11
, pp. 223-229
-
-
Herzberg, O.1
Moult, J.2
-
3
-
-
0030010605
-
Experimentally observed conformation-dependent geometry and hidden strain in proteins
-
Karplus, P.A. (1996). Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci. 5, 1406-1420.
-
(1996)
Protein Sci.
, vol.5
, pp. 1406-1420
-
-
Karplus, P.A.1
-
4
-
-
0025651996
-
Errors in three dimensions
-
Janin, J. (1990). Errors in three dimensions. Biochimie 72, 705-709.
-
(1990)
Biochimie
, vol.72
, pp. 705-709
-
-
Janin, J.1
-
5
-
-
0001644632
-
Between objectivity and subjectivity
-
Branden, C. & Jones, T.A. (1990). Between objectivity and subjectivity. Nature 343, 687-689.
-
(1990)
Nature
, vol.343
, pp. 687-689
-
-
Branden, C.1
Jones, T.A.2
-
6
-
-
0029644940
-
Where freedom is given, liberties are taken
-
Kleywegt, G.J. & Jones, T.A. (1995). Where freedom is given, liberties are taken. Structure 3, 535-540.
-
(1995)
Structure
, vol.3
, pp. 535-540
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
7
-
-
0022333121
-
Stereochemically restrained refinement of macromolecular structures
-
Hendrickson, W.A. (1985). Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 11, 252-270.
-
(1985)
Methods Enzymol.
, vol.11
, pp. 252-270
-
-
Hendrickson, W.A.1
-
8
-
-
0027293559
-
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy
-
Brunger, A.T. & Nilges, M. (1993). Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy. Q. Rev. Biophys. 26, 49-125.
-
(1993)
Q. Rev. Biophys.
, vol.26
, pp. 49-125
-
-
Brunger, A.T.1
Nilges, M.2
-
9
-
-
0027999315
-
Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy
-
MacArthur, M.W., Laskowski, R.A. & Thornton, J.M. (1994). Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Boil. 4, 731-737.
-
(1994)
Curr. Opin. Struct. Boil.
, vol.4
, pp. 731-737
-
-
MacArthur, M.W.1
Laskowski, R.A.2
Thornton, J.M.3
-
10
-
-
0030589514
-
Phi/psi-chology: Ramachandran revisited
-
Kleywegt, G.J. & Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400.
-
(1996)
Structure
, vol.4
, pp. 1395-1400
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
11
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder, J.W. & Richards, P.M. (1987). Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, P.M.2
-
12
-
-
0029101826
-
Recognizing native folds by the arrangement of Hydrophobic and polar residues
-
Huang, E.S., Subbiah, S. & Levitt, M. (1995). Recognizing native folds by the arrangement of Hydrophobic and polar residues. J. Mol. Biol. 252, 709-720.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 709-720
-
-
Huang, E.S.1
Subbiah, S.2
Levitt, M.3
-
13
-
-
0025269891
-
Novel method for the rapid evaluation of packing in protein structures
-
Gregoret, L.M. & Cohen, F.E. (1990). Novel method for the rapid evaluation of packing in protein structures. J. Mol. Biol. 211, 959-974.
-
(1990)
J. Mol. Biol.
, vol.211
, pp. 959-974
-
-
Gregoret, L.M.1
Cohen, F.E.2
-
14
-
-
0030598343
-
Deviations from standard atomic volumes as a quality measure for protein crystal structures
-
Pontius, J., Richelle, J. & Wodak, S.J (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264, 121-136.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 121-136
-
-
Pontius, J.1
Richelle, J.2
Wodak, S.J.3
-
15
-
-
0027542118
-
Quality control of protein models: Directional atomic contact analysis
-
Vriend, G. & Sander, C. (1993). Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. 26, 47-60.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 47-60
-
-
Vriend, G.1
Sander, C.2
-
16
-
-
0030341420
-
A knowledge-based method for protein structure refinement and prediction
-
States, D.G., Agarwal, P., Gaasterland, T., Hunter, L. & Smith, R.F., eds, The AAAI Press, Menlo Park, CA
-
Subramaniam, S., Tcheng, D.K. & Fenton, J.M. (1996). A knowledge-based method for protein structure refinement and prediction. In Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. (States, D.G., Agarwal, P., Gaasterland, T., Hunter, L. & Smith, R.F., eds), pp. 218-229, The AAAI Press, Menlo Park, CA.
-
(1996)
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
, pp. 218-229
-
-
Subramaniam, S.1
Tcheng, D.K.2
Fenton, J.M.3
-
17
-
-
0027180507
-
Verification of protein structure: Patterns of nonbonded atomic interactions
-
Colovos, C. & Yeates, T.O. (1993). Verification of protein structure: patterns of nonbonded atomic interactions. Protein Sci. 2, 1511-1519.
-
(1993)
Protein Sci.
, vol.2
, pp. 1511-1519
-
-
Colovos, C.1
Yeates, T.O.2
-
18
-
-
0026505184
-
Evaluation of protein models by atomic solvation preference
-
Holm, L. & Sander, C. (1992). Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225, 92-105.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 92-105
-
-
Holm, L.1
Sander, C.2
-
19
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
20
-
-
0030339738
-
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
-
Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
-
(1996)
J. Biomol. NMR
, vol.8
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmann, J.A.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
-
21
-
-
0027976029
-
Error detection in Crystallographic models
-
Carson, M., Buckner, T.W., Yang, Z. & Narayana, S.V.L. (1994). Error detection in Crystallographic models. Acta Crystallogr. D50, 900-909.
-
(1994)
Acta Crystallogr.
, vol.D50
, pp. 900-909
-
-
Carson, M.1
Buckner, T.W.2
Yang, Z.3
Narayana, S.V.L.4
-
22
-
-
0021691918
-
An analysis of incorrectly folded protein models: Implications for structure predictions
-
Novotny, J., Bruccoleri, R. & Karplus, M. (1984). An analysis of incorrectly folded protein models: implications for structure predictions. J. Mol. Biol. 177, 787-818.
-
(1984)
J. Mol. Biol.
, vol.177
, pp. 787-818
-
-
Novotny, J.1
Bruccoleri, R.2
Karplus, M.3
-
23
-
-
0023804632
-
Criteria that discriminate between native proteins and incorrectly folded models
-
Novotny, J., Rashin, A.A. & Bruccoleri, R. (1988). Criteria that discriminate between native proteins and incorrectly folded models. Proteins 4, 19-30.
-
(1988)
Proteins
, vol.4
, pp. 19-30
-
-
Novotny, J.1
Rashin, A.A.2
Bruccoleri, R.3
-
24
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl, M.J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
26
-
-
0028318094
-
Factors influencing the ability of knowledge-based potential to identify native sequence-structure matches
-
Kocher, J.-P.A., Rooman, M.J. & Wodak, S.J. (1994). Factors influencing the ability of knowledge-based potential to identify native sequence-structure matches. J. Mol. Biol. 235, 1598-1613.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1598-1613
-
-
Kocher, J.-P.A.1
Rooman, M.J.2
Wodak, S.J.3
-
29
-
-
84986522918
-
ICM: A new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation
-
Abagyan, R.A., Totrov, M.M. & Kuznetsov, D.A. (1994). ICM: a new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comp. Chew. 15, 488-506.
-
(1994)
J. Comp. Chew.
, vol.15
, pp. 488-506
-
-
Abagyan, R.A.1
Totrov, M.M.2
Kuznetsov, D.A.3
-
30
-
-
0027146064
-
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: The correct modeling of an eight-residue loop
-
Borchert, T.V., Abagyan, R., Kishan, K.V.R., Zeelen, J.Ph. & Wierenga, R.K. (1993). The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modeling of an eight-residue loop. Structure 1, 205-213.
-
(1993)
Structure
, vol.1
, pp. 205-213
-
-
Borchert, T.V.1
Abagyan, R.2
Kishan, K.V.R.3
Zeelen, J.Ph.4
Wierenga, R.K.5
-
31
-
-
0027185404
-
A method to configure protein sidechains from the mainchain trace in homology modeling
-
Eisenmenger, F., Argos, P. & Abagyan, R.A. (1993). A method to configure protein sidechains from the mainchain trace in homology modeling. J. Mol. Biol. 231, 849-860.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 849-860
-
-
Eisenmenger, F.1
Argos, P.2
Abagyan, R.A.3
-
32
-
-
0028410583
-
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy
-
Totrov, M.M. & Abagyan, R.A. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nat. Struct. Biol. 1, 259-263.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 259-263
-
-
Totrov, M.M.1
Abagyan, R.A.2
-
33
-
-
0028304890
-
Recognition of distantly related proteins through energy calculations
-
Abagyan, R.A., Frishman, D. & Argos, P. (1994). Recognition of distantly related proteins through energy calculations. Proteins 19, 132-140.
-
(1994)
Proteins
, vol.19
, pp. 132-140
-
-
Abagyan, R.A.1
Frishman, D.2
Argos, P.3
-
34
-
-
0028849881
-
Homology modeling by the ICM method
-
Cardozo, T., Totrov, M. & Abagyan, R. (1995). Homology modeling by the ICM method. Proteins 23, 403-414.
-
(1995)
Proteins
, vol.23
, pp. 403-414
-
-
Cardozo, T.1
Totrov, M.2
Abagyan, R.3
-
35
-
-
0030939896
-
A new method for modeling large-scale rearrangements of protein domains
-
Maiorov, V.N. & Abagyan, R.A. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410-424.
-
(1997)
Proteins
, vol.27
, pp. 410-424
-
-
Maiorov, V.N.1
Abagyan, R.A.2
-
36
-
-
5944250450
-
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
-
Momany, F.A., McGuire, R.F., Burgess, A.W. & Scheraga, H.A. (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79, 2361-2381.
-
(1975)
J. Phys. Chem.
, vol.79
, pp. 2361-2381
-
-
Momany, F.A.1
McGuire, R.F.2
Burgess, A.W.3
Scheraga, H.A.4
-
37
-
-
33845550595
-
Energy parameters in polypeptides. 9. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids
-
Nemethy, G., Pottle, M.S. & Scheraga, H.A. (1983). Energy parameters in polypeptides. 9. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87, 1883-1887.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 1883-1887
-
-
Nemethy, G.1
Pottle, M.S.2
Scheraga, H.A.3
-
38
-
-
0001731773
-
Energy parameters in polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Nemethy, G., et al., & Scheraga, H.A. (1992). Energy parameters in polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96, 6472-6484.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 6472-6484
-
-
Nemethy, G.1
Scheraga, H.A.2
-
39
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan, R.A. & Totrov, M.M. (1994). Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983-1002.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 983-1002
-
-
Abagyan, R.A.1
Totrov, M.M.2
-
40
-
-
0021104997
-
Refined structure of the gene 5-DNA binding protein from bacteriophage FD
-
Brayer, G.D. & McPherson, A. (1993). Refined structure of the gene 5-DNA binding protein from bacteriophage FD. J. Mol. Biol. 169, 565-570.
-
(1993)
J. Mol. Biol.
, vol.169
, pp. 565-570
-
-
Brayer, G.D.1
McPherson, A.2
-
41
-
-
0028325221
-
Structure of the gene V protein of bacteriophage f1 determined by multiwavelength X-ray diffraction on the selenomethionyl protein
-
Skinner, M.M., et al., & Terwilliger, T.C. (1994). Structure of the gene V protein of bacteriophage f1 determined by multiwavelength X-ray diffraction on the selenomethionyl protein. Proc. Natl Acad. Sci. USA 91, 2071-2075.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 2071-2075
-
-
Skinner, M.M.1
Terwilliger, T.C.2
-
42
-
-
0031560777
-
Contact area difference (CAD): A robust measure to evaluate accuracy of protein models
-
Abagyan, R. & Totrov, M. (1997). Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J. Mol. Biol. 268, 678-685.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 678-685
-
-
Abagyan, R.1
Totrov, M.2
-
43
-
-
33646321663
-
Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search
-
Abagyan, R., Batalov, S., Cardozo, T., Totrov, M. & Zhou, Y. (1997). Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. Proteins 30, 1 -9.
-
(1997)
Proteins
, vol.30
, pp. 1-9
-
-
Abagyan, R.1
Batalov, S.2
Cardozo, T.3
Totrov, M.4
Zhou, Y.5
-
44
-
-
0031054817
-
Protein engineering with monomeric triosephosphate isomerase (monoTIM): The modeling and structure verification of a seven-residue loop
-
Thanki, N., et al., & Schliebs, W. (1997). Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modeling and structure verification of a seven-residue loop. Protein Eng. 10, 159-167.
-
(1997)
Protein Eng.
, vol.10
, pp. 159-167
-
-
Thanki, N.1
Schliebs, W.2
-
45
-
-
0028049318
-
Design, creation, and characterization of a stable, monomeric triosephosphate isomerase
-
Borchert, T.V., Abagyan, R.A., Jaenicke, R. & Wierenga, R.K. (1994). Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc. Natl Acad. Sci. USA 91, 1515-1518.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 1515-1518
-
-
Borchert, T.V.1
Abagyan, R.A.2
Jaenicke, R.3
Wierenga, R.K.4
-
46
-
-
0030593678
-
Crystal structure of a caricain D158E mutant in complex with E-64
-
Katerelos, N.A., Taylor, M.A., Scott, M., Goodenough, P.W. & Pickersgill, R.W. (1996). Crystal structure of a caricain D158E mutant in complex with E-64. FEBS Lett. 392, 35-39.
-
(1996)
FEBS Lett.
, vol.392
, pp. 35-39
-
-
Katerelos, N.A.1
Taylor, M.A.2
Scott, M.3
Goodenough, P.W.4
Pickersgill, R.W.5
-
47
-
-
0003035460
-
Structure of monoclinic papain at 1.60 Å resolution
-
Pickersgill, R.W., Harris, G.W. & Garman, E. (1992). Structure of monoclinic papain at 1.60 Å resolution. Acta Crystallogr. B48, 59-62.
-
(1992)
Acta Crystallogr.
, vol.B48
, pp. 59-62
-
-
Pickersgill, R.W.1
Harris, G.W.2
Garman, E.3
-
49
-
-
0000538967
-
Protein structure prediction by global energy optimization
-
(van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J., eds), Kluwer Academic Publishers, London
-
Abagyan, R.A. (1997). Protein structure prediction by global energy optimization. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications. Vol 3. (van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J., eds), Kluwer Academic Publishers, London.
-
(1997)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
, vol.3
-
-
Abagyan, R.A.1
-
50
-
-
0031576355
-
Do aligned sequences share the same fold?
-
Abagyan, R.A. & Batalov, S.V. (1997). Do aligned sequences share the same fold? J. Mol. Biol. 273, 355-368.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 355-368
-
-
Abagyan, R.A.1
Batalov, S.V.2
-
51
-
-
0029645414
-
Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase
-
Georgiadis, M.M., et al., & Hendrickson, W.A. (1995). Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase. Structure 3, 879-892.
-
(1995)
Structure
, vol.3
, pp. 879-892
-
-
Georgiadis, M.M.1
Hendrickson, W.A.2
-
52
-
-
0024609825
-
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles
-
Abagyan, R.A. & Mazur, A.K. (1989). New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6, 833-845.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 833-845
-
-
Abagyan, R.A.1
Mazur, A.K.2
-
53
-
-
0026681839
-
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
-
Abagyan, R.A. & Argos, P. (1992). Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 225, 519-532.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 519-532
-
-
Abagyan, R.A.1
Argos, P.2
-
54
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
-
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|