-
1
-
-
4344586564
-
Homology-based modelling of targets for rational drug design
-
Wieman,H., Tondel,K., Anderssen,E. and Drablos,F. (2004) Homology-based modelling of targets for rational drug design. Mini Rev. Med. Chem., 4, 793-804.
-
(2004)
Mini Rev. Med. Chem
, vol.4
, pp. 793-804
-
-
Wieman, H.1
Tondel, K.2
Anderssen, E.3
Drablos, F.4
-
2
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez,R., Leplae,R., Lensink,M.F. and Wodak,S.J. (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins, 60, 150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
3
-
-
2442677781
-
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
-
Arakaki,A.K., Zhang,Y. and Skolnick,J. (2004) Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics, 20, 1087-1096.
-
(2004)
Bioinformatics
, vol.20
, pp. 1087-1096
-
-
Arakaki, A.K.1
Zhang, Y.2
Skolnick, J.3
-
4
-
-
0032410839
-
Packing of sidechains in low-resolution models for proteins
-
Keskin,O. and Bahar,I. (1998) Packing of sidechains in low-resolution models for proteins. Fold. Des., 3, 469-479.
-
(1998)
Fold. Des
, vol.3
, pp. 469-479
-
-
Keskin, O.1
Bahar, I.2
-
5
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
(Suppl. 7)
-
Kryshtafovych,A., Venclovas,C., Fidelis,K. and Moult,J. (2005) Progress over the first decade of CASP experiments. Proteins, 61(Suppl. 7), 225-236.
-
(2005)
Proteins
, vol.61
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
6
-
-
33847673583
-
Near-native structure refinement using in vacuo energy minimization
-
Summa,C.M. and Levitt,M. (2007) Near-native structure refinement using in vacuo energy minimization. Proc. Natl. Acad. Sci. U.S.A., 104, 3177-3182.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 3177-3182
-
-
Summa, C.M.1
Levitt, M.2
-
7
-
-
84871034858
-
3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization
-
Bhattacharya,D. and Cheng,J. (2013) 3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization. Proteins, 81, 119-131.
-
(2013)
Proteins
, vol.81
, pp. 119-131
-
-
Bhattacharya, D.1
Cheng, J.2
-
8
-
-
84880487307
-
i3Drefine software for protein 3D structure refinement and its assessment in CASP10
-
Bhattacharya,D. and Cheng,J. (2013) i3Drefine software for protein 3D structure refinement and its assessment in CASP10. PLoS One, 8, e69648.
-
(2013)
PLoS One
, vol.8
, pp. e69648
-
-
Bhattacharya, D.1
Cheng, J.2
-
9
-
-
27544480322
-
MESHI: a new library of Java classes for molecular modeling
-
Kalisman,N., Levi,A., Maximova,T., Reshef,D., Zafriri-Lynn,S., Gleyzer,Y. and Keasar,C. (2005) MESHI: a new library of Java classes for molecular modeling. Bioinformatics, 21, 3931-3932.
-
(2005)
Bioinformatics
, vol.21
, pp. 3931-3932
-
-
Kalisman, N.1
Levi, A.2
Maximova, T.3
Reshef, D.4
Zafriri-Lynn, S.5
Gleyzer, Y.6
Keasar, C.7
-
10
-
-
78149453870
-
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction
-
Zhang,J. and Zhang,Y. (2010) A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One, 5, e15386.
-
(2010)
PLoS One
, vol.5
, pp. e15386
-
-
Zhang, J.1
Zhang, Y.2
-
11
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Chen,V.B., Arendall,W.B., Headd,J.J., Keedy,D.A., Immormino,R.M., Kapral,G.J., Murray,L.W., Richardson,J.S. and Richardson,D.C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr., 66, 12-21.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
12
-
-
33646887390
-
On the limited memory BFGS method for large scale optimization
-
Liu,D.C. and Nocedal,J. (1989) On the limited memory BFGS method for large scale optimization. Math. Program., 45, 503-528.
-
(1989)
Math. Program
, vol.45
, pp. 503-528
-
-
Liu, D.C.1
Nocedal, J.2
-
13
-
-
0029633167
-
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt,M., Hirshberg,M., Sharon,R. and Daggett,V. (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput. Phys. Commun., 91, 215-231.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
14
-
-
0042622381
-
LGA: a method for finding 3D similarities in protein structures
-
Zemla,A. (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
15
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
16
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch,W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 32, 922-923.
-
(1976)
Acta Crystallogr. A
, vol.32
, pp. 922-923
-
-
Kabsch, W.1
-
17
-
-
84876239078
-
JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia
-
Hanson,R.M., Prilusky,J., Renjian,Z., Nakane,T. and Sussman,J.L. (2013) JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia. Isreal J. Chem., 53, 207-216.
-
(2013)
Isreal J. Chem
, vol.53
, pp. 207-216
-
-
Hanson, R.M.1
Prilusky, J.2
Renjian, Z.3
Nakane, T.4
Sussman, J.L.5
-
18
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and 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
-
19
-
-
74249121740
-
Assessment of the protein-structure refinement category in CASP8
-
(Suppl. 9)
-
MacCallum,J.L., Hua,L., Schnieders,M.J., Pande,V.S., Jacobson,M.P. and Dill,K.A. (2009) Assessment of the protein-structure refinement category in CASP8. Proteins, 77(Suppl. 9), 66-80.
-
(2009)
Proteins
, vol.77
, pp. 66-80
-
-
MacCallum, J.L.1
Hua, L.2
Schnieders, M.J.3
Pande, V.S.4
Jacobson, M.P.5
Dill, K.A.6
-
20
-
-
82955239912
-
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
-
Zhang,J., Liang,Y. and Zhang,Y. (2011) Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure, 19, 1784-1795.
-
(2011)
Structure
, vol.19
, pp. 1784-1795
-
-
Zhang, J.1
Liang, Y.2
Zhang, Y.3
-
21
-
-
84864436301
-
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
-
Rodrigues,J.P., Levitt,M. and Chopra,G. (2012) KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res., 40, W323-W328.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W323-W328
-
-
Rodrigues, J.P.1
Levitt, M.2
Chopra, G.3
-
22
-
-
84883590772
-
GalaxyRefine: protein structure refinement driven by side-chain repacking
-
Heo,L., Park,H. and Seok,C. (2013) GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res., 41, W384-W388.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. W384-W388
-
-
Heo, L.1
Park, H.2
Seok, C.3
|