TY - JOUR AU - Jones, S. AU - Shanahan, H. P. AU - Berman, H. M. AU - Thornton, J. M. PY - 2003 DA - 2003// TI - Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg922 DO - 10.1093/nar/gkg922 ID - Jones2003 ER - TY - JOUR AU - Shanahan, H. P. AU - Garcia, M. A. AU - Jones, S. AU - Thornton, J. M. PY - 2004 DA - 2004// TI - Identifying DNA-binding proteins using structural motifs and the electrostatic potential JO - Nucl Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh803 DO - 10.1093/nar/gkh803 ID - Shanahan2004 ER - TY - JOUR AU - Tsuchiya, Y. AU - Kinoshita, K. AU - Nakamura, H. PY - 2004 DA - 2004// TI - Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces JO - Proteins VL - 55 UR - https://doi.org/10.1002/prot.20111 DO - 10.1002/prot.20111 ID - Tsuchiya2004 ER - TY - JOUR AU - Gao, M. AU - Skolnick, J. PY - 2008 DA - 2008// TI - DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn332 DO - 10.1093/nar/gkn332 ID - Gao2008 ER - TY - JOUR AU - Keil, M. AU - Exner, T. AU - Brickmann, J. PY - 2004 DA - 2004// TI - Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network JO - J Comput Chem VL - 25 UR - https://doi.org/10.1002/jcc.10361 DO - 10.1002/jcc.10361 ID - Keil2004 ER - TY - JOUR AU - Ahmad, S. AU - Gromiha, M. M. AU - Sarai, A. PY - 2004 DA - 2004// TI - Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg432 DO - 10.1093/bioinformatics/btg432 ID - Ahmad2004 ER - TY - JOUR AU - Tjong, H. AU - Zhou, H. -. X. PY - 2007 DA - 2007// TI - DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces JO - Nucl Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm008 DO - 10.1093/nar/gkm008 ID - Tjong2007 ER - TY - JOUR AU - Xiong, Y. AU - Liu, J. AU - Wei, D. -. Q. PY - 2011 DA - 2011// TI - An accurate feature-based method for identifying DNA-binding residues on protein surfaces JO - Proteins VL - 79 UR - https://doi.org/10.1002/prot.22898 DO - 10.1002/prot.22898 ID - Xiong2011 ER - TY - JOUR AU - Segura, J. AU - Jones, P. F. AU - Fernandez-Fuentes, N. PY - 2012 DA - 2012// TI - A holistic in silico approach to predict functional sites in protein structures JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts269 DO - 10.1093/bioinformatics/bts269 ID - Segura2012 ER - TY - JOUR AU - Yan, C. AU - Terribilini, M. AU - Wu, F. AU - Jernigan, R. L. AU - Dobbs, D. AU - Honavar, V. PY - 2006 DA - 2006// TI - Identifying amino acid residues involved in protein-DNA interactions from sequence JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-262 DO - 10.1186/1471-2105-7-262 ID - Yan2006 ER - TY - JOUR AU - Ahmad, S. AU - Sarai, A. PY - 2005 DA - 2005// TI - PSSM-based prediction of DNA binding sites in proteins JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-33 DO - 10.1186/1471-2105-6-33 ID - Ahmad2005 ER - TY - JOUR AU - Wang, L. AU - Brown, S. J. PY - 2006 DA - 2006// TI - BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences JO - Nucl Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl298 DO - 10.1093/nar/gkl298 ID - Wang2006 ER - TY - JOUR AU - Wang, L. AU - Yang, M. AU - Yang, J. PY - 2009 DA - 2009// TI - Prediction of DNA-binding residues from protein sequence information using random forests JO - BMC Genomics VL - 10 UR - https://doi.org/10.1186/1471-2164-10-S1-S1 DO - 10.1186/1471-2164-10-S1-S1 ID - Wang2009 ER - TY - JOUR AU - Wu, J. AU - Liu, H. AU - Duan, X. AU - Ding, Y. AU - Wu, H. AU - Bai, Y. AU - Sun, X. PY - 2009 DA - 2009// TI - Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn583 DO - 10.1093/bioinformatics/btn583 ID - Wu2009 ER - TY - JOUR AU - Ofran, Y. AU - Mysore, V. AU - Rost, B. PY - 2007 DA - 2007// TI - Prediction of DNA-binding residues from sequence JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm174 DO - 10.1093/bioinformatics/btm174 ID - Ofran2007 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The Protein Data Bank JO - Nucl Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Wang, G. AU - Dunbrack, R. L. J. PY - 2003 DA - 2003// TI - PISCES: a protein sequence culling server JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg224 DO - 10.1093/bioinformatics/btg224 ID - Wang2003 ER - TY - CHAP AU - Hubbard, S. J. PY - 1993 DA - 1993// BT - NACCESS PB - Department of Biochemistry and Molecular Biology, University College CY - London ID - Hubbard1993 ER - TY - JOUR AU - Rocchia, W. AU - Alexov, E. AU - Honig, B. PY - 2001 DA - 2001// TI - Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions JO - J Phys Chem VL - 105 UR - https://doi.org/10.1021/jp010454y DO - 10.1021/jp010454y ID - Rocchia2001 ER - TY - JOUR AU - Sander, C. AU - Schneider, R. PY - 1991 DA - 1991// TI - Database of homology derived protein structures and the structural meaning of sequence alignment JO - Proteins VL - 9 UR - https://doi.org/10.1002/prot.340090107 DO - 10.1002/prot.340090107 ID - Sander1991 ER - TY - JOUR AU - Holm, L. AU - Sander, C. PY - 1995 DA - 1995// TI - Dali: a network tool for protein structure comparison JO - Trends Biochem Sci VL - 20 UR - https://doi.org/10.1016/S0968-0004(00)89105-7 DO - 10.1016/S0968-0004(00)89105-7 ID - Holm1995 ER - TY - JOUR AU - Valdar, W. S. J. PY - 2002 DA - 2002// TI - Scoring residue conservation JO - Proteins: Struct, Funct, Genet VL - 48 UR - https://doi.org/10.1002/prot.10146 DO - 10.1002/prot.10146 ID - Valdar2002 ER - TY - JOUR AU - Altschul, S. AU - Madden, T. AU - Schaffer, A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucl Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - CHAP AU - Borgwardt, K. M. AU - Kriegel, H. P. PY - 2005 DA - 2005// TI - Shortest-path kernels on graphs BT - The fifth IEEE International Conference on Data Minning (ICDM'05) UR - https://doi.org/10.1109/ICDM.2005.132 DO - 10.1109/ICDM.2005.132 ID - Borgwardt2005 ER - TY - JOUR AU - Borgwardt, K. M. AU - Ong, C. S. AU - Schonauer, S. AU - Vishwanathan, S. V. N. AU - Smola, A. J. AU - Kriegel, H. P. PY - 2005 DA - 2005// TI - Protein function prediction via graph kernels JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1007 DO - 10.1093/bioinformatics/bti1007 ID - Borgwardt2005 ER -