ColabFold - Making protein folding accessible to all
Year: 2021
Type: preprint
Abstract: ColabFold 1.6.3 Highlights: ColabFold can now be fully installed from pip. Turing/Volta generation GPUs are now much faster with --use-fast-kernels. ColabFold now computes and displays ipSAE/pDockQ2. Bug fixes --use-pallas produced wrong results in 1.6.2 Head dimensions below 16 (the extra MSA stack) computed a wrong dot product on NVIDIA GPUs, and the key mask was read from the first row only, leaving template pointwise attention unmasked. (9b67373) Fix --msa-mode single_sequence using one additional randomly picked homolog per seed when the input is an a3m file or a cached MSA, instead of the query alone (8d4aefe) Fix colabfold_search leaving per-chain a3m stubs behind in paired mode (99a9868) Fix --initial-guess compiling the model a second time (9b67373) New features and enhancements Fused kernels for Turing and Volta GPUs New --kernel-backend flag (auto (default), pallas, cuda_legacy) selects the fused Evoformer implementation (~2x faster on V100; 343b72d, 9b67373, 97ca370, 785b4fa) --use-fast-kernels replaces --use-pallas. --use-pallas keeps working (f7e9d49) ipSAE and pDockQ2 interface scores are reported for complexes (0c788a0) Thanks @Gyuuul2 Lower Evoformer memory Transition subbatching is sized to a 256 MiB intermediate rather than 4 rows, and head-8 attention no longer pads q/k/v to 16 (9b67373) kalign, hhsearch and openmm from pip No conda needed for the local install (334057d, a2ce769)
Authors: Sergey Ovchinnikov, Martin Steinegger, Milot Mirdita, konsti, Yoshitaka Moriwaki, Rachel Seongeun Kim, Phil Wang, Jan Kosinski, Tadej Satler, PhD, Sooyoung Cha, Kieran Didi, Enzo Guerrero-Araya, teodorpopescuQB, Lim Heo, Abhishaike Mahajan, LiorZ, Magnus Haraldson Høie, Milind Jagota, Pasquale Miglionico, Ramon Crehuet, Siddharth Betala, Sven Giese, Theo Sternlieb, Thomas Holder, Wahab Kawafi, Yossi Eliaz, heya5, tlitfin, Kevin Pan, Kevin Dalton
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6950304745