MIBPB swMATH ID: 8106 Software Authors: Duan Chen; Zhan Chen; Changjun Chen; Weihua Geng; Guo-Wei Wei Description: MIBPB: A software package for electrostatic analysis. The Poisson–Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)-based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique-based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second-order convergence, that is, the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-to-Neumann mapping technique that builds a Green’s function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1 Å — whereas it usually takes other traditional PB solvers 0.25 Å to reach similar level of reliability. This work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by using the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate KS solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein–solvent solvation energy calculations and analysis of salt effects on protein–protein binding energies, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011 Homepage: http://www.math.msu.edu/~wei/MIBPB/ Related Software: APBS; tabipb; PDB2PQR; TABI; CHARMM; PBEQ-Solver; TMSmesh; AFMPB; SDPBS; DelPhi Web Server; IIMPACK; FEniCS; SMPBS; DelPhi; UHBD; Apbsmem; PETSc; AMBER; PyGBe; DelPhiPKa Cited in: 60 Documents all top 5 Cited by 95 Authors 20 Wei, Guowei 11 Xia, Kelin 11 Zhao, Shan 9 Geng, Weihua 8 Chen, Duan 5 Chen, Zhan 5 Xie, Dexuan 4 Alexov, Emil 4 Mu, Lin 4 Ying, Jinyong 3 Chen, Jiahui 3 Wang, Bao 3 Zhan, Meng 3 Zheng, Qiong 2 Baker, Nathan A. 2 Egan, Raphael 2 Gibou, Frédéric 2 Hu, Jingzhen 2 Hu, Langhua 2 Krasny, Robert 2 Lu, Benzhuo 2 Tong, Yiying 2 Ullah, Sheik Ahmed 2 Wang, Junping 2 Wang, Siwen 2 Ye, Xiu 1 Abbaszadeh, Mostafa 1 Bardhan, Jaydeep P. 1 Bochkov, Daniil 1 Cang, Zixuan 1 Cao, Yin 1 Chen, Huangxin 1 Chen, Long 1 Chen, Minhong 1 Chowdhury, Rochishnu 1 Davydov, Oleg V. 1 Debuhr, Jackson 1 Dehghan Takht Fooladi, Mehdi 1 Deng, Weishan 1 Dou, Wei 1 Feng, Xin 1 Han, Yihui 1 Hazra, Tania 1 Hou, Songming 1 Jacob, Ferosh 1 Jiang, Yi 1 Jo, Gwanghyun 1 Knepley, Matthew G. 1 Kreienkamp, Amelia B. 1 Kuang, Ying 1 Kwak, Do Young 1 Kwon, In-Hyuk 1 Lee, Arum 1 Li, Chuan 1 Li, Jiao 1 Li, Lin 1 Liu, Kaifang 1 Liu, Lucy Y. 1 Maday, Yvon 1 Mayolo, Silvio 1 Minkara, Mona S. 1 Niedzielski, Drake 1 Opron, Kristopher 1 Petukh, Marharyta 1 Quan, Chaoyu 1 Radhakrishnan, Mala L. 1 Ren, Kui 1 Rocchia, Walter 1 Safarpoor, Mansour 1 Sarkar, Subhra 1 Shao, Yuanzhen 1 Shi, Liwei 1 Song, Lunji 1 Stamm, Benjamin 1 Sterling, Thomas Lawrence 1 Tsai, Yen-Hsi Richard 1 Wan, Decheng 1 Wang, Menglun 1 Wang, Xiaoping 1 Wei, Huayi 1 Wen, Min 1 Wilson, Leighton 1 Witham, Shawn 1 Wu, Kedi 1 Xie, Xiaoping 1 Xie, Yang 1 Xu, Jin 1 Yang, Siyang 1 Yu, Zeyun 1 Zhang, Bo 1 Zhang, Jie 1 Zhao, Rundong 1 Zhenirovskyy, Maxim 1 Zhong, Yimin 1 Zhou, Shenggao all top 5 Cited in 20 Serials 23 Journal of Computational Physics 7 Molecular Based Mathematical Biology 5 Journal of Computational and Applied Mathematics 3 Bulletin of Mathematical Biology 3 Communications in Computational Physics 2 Computer Physics Communications 2 Journal of Mathematical Biology 2 Applied Numerical Mathematics 2 International Journal for Numerical Methods in Biomedical Engineering 1 Computers & Mathematics with Applications 1 Computer Methods in Applied Mechanics and Engineering 1 Applied Mathematics and Computation 1 Journal of Scientific Computing 1 Applied Mathematical Modelling 1 SIAM Review 1 SIAM Journal on Scientific Computing 1 Communications in Information and Systems 1 International Journal of Numerical Analysis and Modeling 1 Advances in Applied Mathematics and Mechanics 1 Computational and Mathematical Biophysics all top 5 Cited in 12 Fields 38 Numerical analysis (65-XX) 33 Biology and other natural sciences (92-XX) 27 Partial differential equations (35-XX) 10 Optics, electromagnetic theory (78-XX) 4 Computer science (68-XX) 4 Mechanics of deformable solids (74-XX) 2 Differential geometry (53-XX) 2 Quantum theory (81-XX) 2 Statistical mechanics, structure of matter (82-XX) 1 Algebraic topology (55-XX) 1 Systems theory; control (93-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year