├── LICENSE └── README.md /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 Jiaqi 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # AwsomeCADD 2 | 3 | 标题少了一个e，可能是世界潜在地告诉我学习CADD不是那么easy。 4 | 5 | 收集了一些CADD教程，资源总结 6 | 7 | 如有疏漏，烦请指正，邮箱：luskyqi@outlook.com 8 | 9 | 感谢@Tong-Du 的贡献 10 | 11 | ## 目录 12 | - [药物设计综合软件](#药物设计综合软件) 13 | - [三维可视化工具](#三维可视化工具) 14 | - [小分子对接](#小分子对接) 15 | - [分子动力学模拟](#分子动力学模拟) 16 | - [蛋白设计](#蛋白设计) 17 | - [量化](#量化) 18 | - [常用代码包](#常用代码包) 19 | - [其余教程资源总结](#其余教程资源总结) 20 | 21 | ## 药物设计综合软件 22 | 23 | 1. Schrödinger：薛定谔公司，https://www.schrodinger.com/ 24 | 25 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 26 | | ------ | --------- | -------- | -------- | -------- | -------- | 27 | | 钰沐菡 | 视频 | 钰沐菡 | 暂无 | 钰沐菡 | 暂无 | 28 | | 利刃君 | 视频+图文 | 叮当学术 | 叮当学术 | 叮当学术 | 暂无 | 29 | 30 | 2. Discovery Studio：https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/ 31 | 32 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 33 | | -------- | --------- | ------------------- | -------- | -------- | ------------------- | 34 | | 利刃君 | 视频+图文 | 叮当学术 | 叮当学术 | 叮当学术 | 暂无 | 35 | | 纽普生物 | 视频+图文 | 结构生物学-纽普生物 | 暂无 | 暂无 | https://novopro.cn/ | 36 | 37 | 3. CCDC套装：剑桥晶体数据库，各个大学和科研机构购买的较多，https://www.ccdc.cam.ac.uk/ 38 | 39 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 40 | | ------------ | --------- | ------------ | ------------ | ------- | ------------------------ | 41 | | ZeroDesigner | 视频+图文 | ZeroDesigner | ZeroDesigner | DrugScience | https://zerodesigner.cn/ | 42 | 43 | ## 三维可视化工具 44 | 45 | 1. PyMol：分为开源和免费两个版本，建议从官网下载：https://pymol.org/2/，官网教程：https://pymolwiki.org/index.php/Main_Page 46 | 47 | + 论文： 48 | 1. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC. 49 | 50 | 51 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 52 | | ------------ | --------- | ------------ | -------------------------------- | ------------------ | -------------------------------- | 53 | | ZeroDesigner | 视频+图文 | ZeroDesigner | ZeroDesigner | DrugScience | https://zerodesigner.cn/ | 54 | | 钰沐菡 | 视频 | 钰沐菡 | 暂无 | 钰沐菡 | 暂无 | 55 | | 北极星max | 视频 | 北极星max | 暂无 | 暂无 | 暂无 | 56 | | 甜橙zzz | 视频 | 甜橙zzz | 暂无 | 暂无 | 暂无 | 57 | | autolife | 图文 | 暂无 | 暂无 | 暂无 | http://pymol.chenzhaoqiang.com/# | 58 | | I_am_Becky | 视频+图文 | I_am_Becky | Becky 学习生物分析软件和文献阅读 | Becky的生活and科研 | 暂无 | 59 | 60 | 2. Chimera：开源 ，http://www.cgl.ucsf.edu/chimera/，官网使用手册：http://www.cgl.ucsf.edu/chimera/docindex.html 61 | 62 | + 论文： 63 | 1. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct;25(13):1605-12. doi: 10.1002/jcc.20084. PMID: 15264254. 64 | 65 | 66 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 67 | | ------ | ---- | ------ | ---- | ------ | -------- | 68 | | 钰沐菡 | 视频 | 钰沐菡 | 暂无 | 钰沐菡 | 暂无 | 69 | 70 | 3. VMD：开源，https://www.ks.uiuc.edu/Research/vmd/ 71 | 72 | + 论文： 73 | 1. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996 Feb;14(1):33-8, 27-8. doi: 10.1016/0263-7855(96)00018-5. PMID: 8744570. 74 | 75 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 76 | | ------ | ---- | ---- | ---- | ------ | ----------------------------------- | 77 | | 李继存 | 图文 | 暂无 | 暂无 | 暂无 | https://jerkwin.github.io/tags/#vmd | 78 | 79 | ## 小分子对接 80 | 81 | 1. Vina：官网：http://vina.scripps.edu/ 82 | 83 | + 论文： 84 | 1. Vina 1.2.0: Eberhardt J, Santos-Martins D, Tillack A, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. ChemRxiv. Cambridge: Cambridge Open Engage; 2021; This content is a preprint and has not been peer-reviewed. 85 | 2. Vina 1.1.2 :Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010 Jan 30;31(2):455-61. doi: 10.1002/jcc.21334. PMID: 19499576; PMCID: PMC3041641. 86 | 87 | 88 | 3. AutoDock：官网：http://autodock.scripps.edu/ 89 | 90 | + 论文： 91 | 1. AutoDock 4.2：Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91. 92 | 2. AutoDock 3 & 4：Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Computational Chemistry, 19: 1639-1662. 93 | 3. AutoDock 4 Scoring Function：Huey, R., Morris, G. M., Olson, A. J. and Goodsell, D. S. (2007), A Semiempirical Free Energy Force Field with Charge-Based Desolvation J. Computational Chemistry, 28: 1145-1152. 94 | 4. AutoDock 2.4：Morris, G. M., Goodsell, D. S., Huey, R. and Olson, A. J. (1996), Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 J. Computer-Aided Molecular Design, 10: 293-304. 95 | 5. AutoDock 1：Goodsell, D. S. and Olson, A. J. (1990), Automated Docking of Substrates to Proteins by Simulated Annealing Proteins:Structure, Function and Genetics., 8: 195-202. 96 | 97 | 98 | 99 | 5. DOCK：官网：http://dock.compbio.ucsf.edu/ 100 | 101 | + 论文： 102 | 1. DOCK 6: Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem. 2015 Jun 5;36(15):1132-56. doi: 10.1002/jcc.23905. PMID: 25914306; PMCID: PMC4469538. 103 | 2. DOCK 3: Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 1985 Jul;28(7):849-57. doi: 10.1021/jm00145a002. PMID: 3892003. 104 | 7. LeDock：官网：http://www.lephar.com/software.htm 105 | 106 | + 论文： 107 | 1. 引用文献，非原始文献：Lee A, Kim D. CRDS: Consensus Reverse Docking System for target fishing. Bioinformatics. 2020 Feb 1;36(3):959-960. doi: 10.1093/bioinformatics/btz656. PMID: 31432077. 108 | 109 | 9. GOLD：属于CCDC套装，官网：https://www.ccdc.cam.ac.uk/ 110 | 111 | + 论文： 112 | 1. GOLD_2:Verdonk, Marcel & Cole, Jason & Hartshorn, Michael & Murray, Christopher & Taylor, Richard. (2003). Improved Protein–ligand docking using GOLD. Proteins. 52. 609-23. 10.1002/prot.10465. 113 | 2. GOLD_1:J ones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997 Apr 4;267(3):727-48. doi: 10.1006/jmbi.1996.0897. PMID: 9126849. 114 | 3. CHEMPLP：Korb O, Stützle T, Exner TE. Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model. 2009 Jan;49(1):84-96. doi: 10.1021/ci800298z. PMID: 19125657. 115 | 116 | 117 | 6. Glide：属于薛定谔：https://www.schrodinger.com/ 118 | 119 | + 论文： 120 | 1. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004 Mar 25;47(7):1739-49. doi: 10.1021/jm0306430. PMID: 15027865. 121 | 122 | 123 | 8. cdocker：属于DiscoveryStudio，官网：https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/ 124 | 125 | + 论文： 126 | 1. Gagnon JK, Law SM, Brooks CL 3rd. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. J Comput Chem. 2016 Mar 30;37(8):753-62. doi: 10.1002/jcc.24259. Epub 2015 Dec 21. PMID: 26691274; PMCID: PMC4776757. 127 | 128 | | ID | 类型 | Vina | AutoDock | DOCK | LeDock | GOLD | XP，SP | cdocker | 129 | | ------------ | --------- | ---- | -------- | ---- | ------ | ---- | ------ | ------- | 130 | | ZeroDesigner | 视频+图文 | ✔️ | ✖️ | ✔️ | ✔️ | ✔️ | ✖️ | ✖️ | 131 | | 钰沐菡 | 视频 | ✔️ | ✔️ | ✖️ | ✖️ | ✖️ | ✔️ | ✖️ | 132 | | 利刃君 | 视频+图文 | ✖️ | ✖️ | ✖️ | ✖️ | ✖️ | ✖️ | ✔️ | 133 | 134 | ## 分子动力学模拟 135 | 136 | 1. Gromacs：官网：www.gromacs.org 137 | 138 | + 论文： 139 | 1. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem. 2005 Dec;26(16):1701-18. doi: 10.1002/jcc.20291. PMID: 16211538. 140 | 141 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 142 | | ---------- | --------- | ---------- | -------------------------------- | ------------------ | -------------------------- | 143 | | 李继存 | 图文 | 暂无 | 暂无 | 暂无 | https://jerkwin.github.io/ | 144 | | I_am_Becky | 视频+图文 | I_am_Becky | Becky 学习生物分析软件和文献阅读 | Becky的生活and科研 | 暂无 | 145 | | LadPhile | 视频 | LadPhile | 暂无 | 暂无 | 暂无 | 146 | 147 | 2. Amber：官网：http://ambermd.org/ 148 | 149 | + 论文： 150 | 1. R. Salomon-Ferrer, D.A. Case, R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198-210 (2013). 151 | 152 | 暂无，待补充 153 | 154 | 3. NAMD：官网：https://www.ks.uiuc.edu/Research/namd/ 155 | 156 | + 论文： 157 | 1. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005. 158 | 159 | 160 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 161 | | -------------- | --------- | ---- | -------------- | ------ | -------- | 162 | | BlueBottleBite | 视频+图文 | 暂无 | BlueBottleBite | 暂无 | 暂无 | 163 | 164 | 165 | 4. OpenMM：官网：https://openmm.org/ 166 | 167 | 168 | + 论文： 169 | 1. Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. PMID: 28746339; PMCID: PMC5549999. 170 | 171 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 172 | | ------------ | --------- | ------------ | ------------ | ------- | ------------------------ | 173 | | ZeroDesigner | 视频+图文 | ZeroDesigner | ZeroDesigner | DrugScience | https://zerodesigner.cn/ | 174 | 175 | 5. Charmm：官网：https://www.charmm.org 176 | 177 | 暂无 178 | 179 | 6. Desmond：官网：https://www.deshawresearch.com/resources_desmond.html 180 | 181 | + 论文： 182 | 1. https://www.deshawresearch.com/publications.html 183 | 184 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 185 | | -------------- | --------- | ---- | -------------- | ------ | -------- | 186 | | BlueBottleBite | 视频+图文 | 暂无 | BlueBottleBite | 暂无 | 暂无 | 187 | 188 | 暂无，待补充 189 | 190 | 7. Schrödinger：官网：薛定谔公司，https://www.schrodinger.com/ 191 | 192 | 暂无，待补充 193 | 194 | 8. Discovery Studio：官网：https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/ 195 | 196 | 暂无，待补充 197 | 198 | ## 蛋白设计 199 | 200 | 1. Rosetta 201 | 202 | + 论文： 203 | 1. http://new.rosettacommons.org/docs/latest/getting_started/Rosetta-canon 204 | 205 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 206 | | ------ | --------- | ---- | ---- | ------------- | --------------------- | 207 | | 吴炜坤 | 视频+图文 | 暂无 | 谷雨 | ROSETTA研习社 | http://139.155.25.244 | 208 | 209 | 2. AlphaFold 210 | 211 | + 论文： 212 | 1. Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021). https://doi.org/10.1038/s41586-021-03819-2 213 | 214 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 215 | | ------ | --------- | ---- | ---- | ------ | --------------------- | 216 | | Sergey | 视频+图文 | 暂无 | 暂无 | 暂无 | http://site.solab.org | 217 | 218 | 仅有B站链接：https://www.bilibili.com/video/BV1Yg411L7Sh 219 | 220 | ## 量化 221 | 222 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | 223 | | ---- | -------- | ---- | ---- | ------ | ---------------------- | 224 | | 卢天 | 线下教学 | 暂无 | 暂无 | 暂无 | http://www.keinsci.com | 225 | 226 | ## 常用代码包 227 | 228 | 1. Rdkit：C++，python，官网：https://rdkit.org 229 | 230 | + 论文： 231 | 1. RDKit: Open-source cheminformatics; http://www.rdkit.org 232 | 233 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | CSDN | 234 | | ------------ | ---- | ------------ | --------------------------------------------------------- | ------- | ------------------------ | ------------ | 235 | | AspirinCode | 图文 | 暂无 | [Aspirin](https://www.zhihu.com/people/wang-jian-min-113) | DrugAI | 暂无 | DrugAI | 236 | | ZeroDesigner | 图文 | ZeroDesigner | ZeroDesigner | DrugScience | https://zerodesigner.cn/ | ZeroDesigner | 237 | 238 | 2. OpenBabel:官网：http://openbabel.org/wiki/Main_Page 239 | 240 | + 论文： 241 | 1. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33. PMID: 21982300; PMCID: PMC3198950. 242 | 243 | | ID | 类型 | B站 | 知乎 | 公众号 | 个人网站 | CSDN | 244 | | ------------ | ---- | ------------ | --------------------------------------------------------- | ------- | ------------------------ | ------------ | 245 | | AspirinCode | 图文 | 暂无 | [Aspirin](https://www.zhihu.com/people/wang-jian-min-113) | DrugAI | 暂无 | DrugAI | 246 | | ZeroDesigner | 图文 | ZeroDesigner | ZeroDesigner | DrugScience | https://zerodesigner.cn/ | ZeroDesigner | 247 | 248 | 249 | ## 其余教程资源总结 250 | 251 | 1. 一系列开源的化学信息学资源：https://github.com/PatWalters/resources/blob/main/cheminformatics_resources.md 综合性较强，内含博客，教程，ML，Python工具等等，英文 252 | 2. teachopencadd：https://github.com/volkamerlab/TeachOpenCADD 如果你是新手接触CADD，可以从这里入手，由初学者为了初学者创建，有paper 英文 253 | --------------------------------------------------------------------------------