-
1
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
47349110113
-
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins
-
DOI 10.1002/prot.21976
-
Vallat BK, Pillardy J, Elber R. A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins. Proteins 2008;72:910-928. (Pubitemid 352000869)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.3
, pp. 910-928
-
-
Vallat, B.K.1
Pillardy, J.2
Elber, R.3
-
3
-
-
38049034590
-
Comparative protein structure modeling with modeller
-
5.6
-
Eswar N, Mari-Renom M, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A. Comparative protein structure modeling with modeller. Curr Protoc Bioinformatics 2006;5.6:5.6.1-5.6.30.
-
(2006)
Curr Protoc Bioinformatics
-
-
Eswar, N.1
Mari-Renom, M.2
Webb, B.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.6
Pieper, U.7
Sali, A.8
-
4
-
-
33644837197
-
SSALN: An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
-
DOI 10.1002/prot.20854
-
Qiu J, Elber R. SSALN: An alignment algorithm using structuredependent substitution matrices and gap penalties learned from structurally aligned protein pairs. Proteins 2006;62:881-891. (Pubitemid 43364153)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.62
, Issue.4
, pp. 881-891
-
-
Qiu, J.1
Elber, R.2
-
5
-
-
0028961335
-
SCOP - A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP - a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
6
-
-
34547434147
-
Support vector training of protein alignment models
-
Research in Computational Molecular Biology - 11th Annual International Conference, RECOMB 2007, Proceedings
-
Chun-Nam JY, Thorsten J, Elber R. Support Vector Training of Protein Alignment Models. Lecture notes in bioinformatics: RECOMB 2007, 2007. (Pubitemid 47164545)
-
(2007)
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4453 LNBI
, pp. 253-267
-
-
Yu, C.-N.J.1
Joachims, T.2
Elber, R.3
Pillardy, J.4
-
7
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
DOI 10.1093/nar/gki524
-
Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309. (Pubitemid 41439897)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
8
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
-
Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 2005;15:285-289. (Pubitemid 40826447)
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.3 SPEC. ISS
, pp. 285-289
-
-
Moult, J.1
-
9
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
DOI 10.1002/prot.20740
-
Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61:225-236. (Pubitemid 43069977)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.SUPPL. 7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
10
-
-
4043052866
-
Accurate prediction of solvent accessibility using neural networks-based regression
-
DOI 10.1002/prot.20176
-
Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 2004;56:753-767. (Pubitemid 39063318)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.4
, pp. 753-767
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
11
-
-
17844392864
-
Combining prediction of secondary structure and solvent accessibility in proteins
-
DOI 10.1002/prot.20441
-
Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005;59:467-475. (Pubitemid 40594291)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.3
, pp. 467-475
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
12
-
-
0020997912
-
Dictionary of protein secondary structure- Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure- pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
13
-
-
0035889689
-
Linear programming optimization and a double statistical filter for protein threading protocols
-
DOI 10.1002/prot.1145
-
Meller J, Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins: Struct Funct Genet 2001;45:241-261. (Pubitemid 32988586)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.45
, Issue.3
, pp. 241-261
-
-
Meller, J.1
Elber, R.2
-
14
-
-
23044531267
-
Protein recognition by sequence-to-structure fitness: Bridging efficiency and capacity of threading models
-
Friesner RA, editor. New York: Wiley
-
Meller J, Elber R. Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models. In: Friesner RA, editor. Computational methods for protein folding: a special volume of advances in chemical physics, Vol.20. New York: Wiley; 2002. pp 77-130.
-
(2002)
Computational Methods for Protein Folding: A Special Volume of Advances in Chemical Physics
, vol.20
, pp. 77-130
-
-
Meller, J.1
Elber, R.2
-
15
-
-
25644439091
-
Calibrating E-values for hidden Markov models using reverse-sequence null models
-
DOI 10.1093/bioinformatics/bti629
-
Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 2005;21:4107-4115. (Pubitemid 41672100)
-
(2005)
Bioinformatics
, vol.21
, Issue.22
, pp. 4107-4115
-
-
Karplus, K.1
Karchin, R.2
Shackelford, G.3
Hughey, R.4
-
16
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
17
-
-
24344479166
-
Atomically detailed potentials to recognize native and approximate protein structures
-
Jian Qiu, Ron Elber. Atomically detailed potentials to recognize native and approximate protein structures. Proteins 2005;61:44-55.
-
(2005)
Proteins
, vol.61
, pp. 44-55
-
-
Qiu, J.1
Elber, R.2
-
18
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
DOI 10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U
-
Tobi D, Elber R. Distance dependent, pair potential for protein folding: Results from linear optimization. Proteins 2000;41:40-116 (Pubitemid 30666911)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.41
, Issue.1
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
19
-
-
84860160829
-
A coarse grained potential for fold recognition and molecular dynamics simulations of proteins
-
in press
-
Májek P, Elber R. A coarse grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins, in press.
-
Proteins
-
-
Májek, P.1
Elber, R.2
-
20
-
-
4744376072
-
On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations
-
Adamczak R, Meller J. On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations. Mol Phys 2004;102:1291-1305.
-
(2004)
Mol Phys
, vol.102
, pp. 1291-1305
-
-
Adamczak, R.1
Meller, J.2
-
22
-
-
1842857770
-
Large-scale linear programming techniques for the design of protein folding potentials
-
Wagner M, Meller J, Elber R. Large-scale linear programming techniques for the design of protein folding potentials. Math Program 2004;101:301-318.
-
(2004)
Math Program
, vol.101
, pp. 301-318
-
-
Wagner, M.1
Meller, J.2
Elber, R.3
-
23
-
-
0037079580
-
Maximum feasibility guideline in the design and analysis of protein folding potentials
-
DOI 10.1002/jcc.10014
-
Meller J, Wagner M, Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. J Comput Chem 2002;23:111-118. (Pubitemid 34063135)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.1
, pp. 111-118
-
-
Meller, J.1
Wagner, M.2
Elber, R.3
|